My own Samus Metroid Backstory



(Here is my own story idea for Samus' story, which basically serves as my rewrite of Other M and my pitch for Metroid Prime 4. Of course, since I'm not that much of a fan of subtle puzzle-solving, my version of Prime 4 looks more like a Star Wars movie rather than a typical Metroid experience. Oh well, I suppose it's my habit of turning everything into Star Wars, I guess.........)

BACKSTORY

Samus Aran, the female human bounty hunter with the Chozo armor, has lived a conflicted and harrowed life. After a Zebesian space pirate attack destroyed her family, she was adopted by a species of bird-men known as the Chozo. After getting training from the Chozo and getting some choice body modifications that turned her into a supersoldier, Samus received a suit of armor from the Chozo as a gift, and soon, she became a warrior in her own right, before the Chozo got killed. After an abortive career as a military space trooper, Samus went into bounty hunting. She found that bounty hunting was a more liberating job, as not only did she pocket money after every mission, but she was able to take any mission she so desired.

Samus’ quest was to stop the Zebesian space pirates from weaponizing Chozo bio-weapons known as the Metroids, energy-parasites that were designed to kill another parasite known as the X-Parasite. The pirates had help from the traitorous Chozo super-computer, Mother Brain, who helped the pirates hunt down and kill off Samus’ Chozo trainers. Samus tried to get the military to take them out, but she felt like they never focused hard enough on taking them out. Hence why she chose the life of a freelance mercenary. As a bounty hunter, Samus would have free reign to pursue the space pirates who killed by her real parents and her adoptive ones. She would have free reign to try and stop their Metroid experiments on her own. And she would be able to fight this war with no civilians or military superiors getting in the way.

Through the years, Samus won several victories over the Zebesian leaders: Mother Brain, the traitorous Chozo super-computer, Ridley, the killer of her parents. Kraid, the repulsive giant. But no matter the amount of victories, Samus felt hollow due to the fact that none of these victories were permanent. They always came back no matter how many times Samus tried to put them down for good. It began to look like these problematic foes would plague her existence forever.

METROID PRIME TRILOGY

During one exploration trip where she intercepted a call from a frigate named Orpheon, Samus was drawn to a world named Talon IV. There she discovered that the pirates were no longer content to play with metroids alone. Through her vast travels in the Chozo planet of Tallon IV, she discovered their old ruins in the world speaking of a prophecy. However, she also discovered that Ridley’s space pirates have been toying with a new element called Phazon, related to the prophecy that the ruins foretold.

Phazon was a powerful but dangerous power source. The space pirates sought to use it as a weapon to enhance their soldiers and metroids. Their experiments yielded successful results, though the infected metroids turned on them as they usually did in these experiments. However, the phazon created a new breed of metroid: the Metroid Prime. The prophecy spoke of how Samus, a Chozo warrior, would bring down the threat of phazon. The phazon had raised the spirits of the Chozo and turned them into rabid animals, and once Samus defeats this Metroid Prime, they will be at rest. Following the example of the pirates, Samus enhanced her suit with phazon, to further empower herself for the trials ahead.

Samus eventually confronted and crushed Metroid Prime, but only after a harrowing battle with it and her old rival Ridley. And after the battle, the Metroid Prime reached into Samus’ phazon-enhanced battlesuit and created for itself a body based on that of Samus Aran. As Samus left, this new creature, Dark Samus, came into being. It then went off on its own following the space pirates and their experiments.

Samus then visited a world called Aether, after receiving a distress signal summoning her there. Arriving at a base of Federation troops, she found them all dead, and sought out what could have done this. Inspecting the base, she finds a new, darker enemy referred to by the ruins of Aether as the Ing. The Ing reanimated the dead Federation troopers and turned them against Samus. Aside from the dead Federation troopers, the space pirates and Dark Samus, the Ing represented the greatest threat on the planet. Samus made an ally of the native Luminoth to help combat the threat. With the help of the Luminoth, Samus discovered that Aether was split between two realms: thanks to the presence of phazon. Dark Aether was ruled by the Ing, while Aether was the regular world.

With the help of the Luminoth, Samus defeated the Ing, and she also defeated Dark Samus several times to ensure that the latter would not make the most of this chaos. Samus defeated the Ing Emperor in his own hive, causing the collapse of Dark Aether. After a brief fight with Dark Samus as she escaped, Samus got back to Aether in triumph, after saving the Luminoth from the darker half of their world. However, Dark Samus survived and escaped Dark Aether as well, and she left to cause her own brand of trouble for the galaxy…..

Samus was once again summoned by another distress call, but this time, it was by a Federation Admiral, Castor Dane, who has assembled a task force to deal with the phazon-infected pirates at last. The latter had been attacking Aurora units, supercomputers used for planetary government, military, and economic tasks. And it seems that Samus was not the only mercenary Dane called for. Samus came into contact with other hunters-friends of hers from when she first started her life as an independent bounty hunter. Gandrayda, Ghor, and Rundas joined her on Dane’s flagship. Gandrayda even made fun of Samus by using her powers to impersonate Samus on Dane’s bridge, before Dane told her to quit it.

Dane’s men were amazed at Samus, whose accomplishments dwarfed those of the other hunters. She made her case to Dane that these phazon-powered pirates are a great threat to the regular troopers that aren’t as experienced at fighting space pirates as she was. But just before they could finish the briefing, a space pirate fleet jumps in and attacks. The fleet was supported by a laser cannon on the nearby planet, which allowed for strikes against orbital targets. After she mopped up the boarders, Samus and the other hunters went down towards the planet to engage the space pirates gathered there.

The assault went well, but Samus had to deal with Ridley again. After battling him in a falling pit, Samus then waltzed over to the laser cannon. Sensing that the tide had turned, the pirates instead opted to crash a massive asteroid filled with phazon energy into the planet. Samus was able to redirect the laser to the asteroid, just in time to destroy it. But as she and her hunter friends gathered for a celebration, Dark Samus attacked. She blasted them with phazon then left the premises after they were all knocked unconscious.

Samus awoke to find herself in a Federation laboratory, wearing a new suit of armor unlike her old one. Samus got an explanation from the Federation officer that was present. Apparently, her body now produces its own natural phazon, and to make use of it, she was given a new suit of armor that can use that energy in combat. Samus was shocked at the notion that she was now a walking talking phazon factory, but she decided that she might as well make use of her new gifts.

Her friends, the other hunters, had gone off to hunt down Dark Samus while she was unconscious. They were rather angry with her after what happened to Samus, so they opted not to wait for her to wake up to head out. Samus was shocked that her friends would do something so rash, so she followed them to lend some aid. Dark Samus was her enemy, her nemesis, and she thought correctly that they have no chance against her, especially when they split up to different worlds to try and find her. Dark Samus was a being of pure phazon energy, one unlike the many criminals and lawbreakers that her friends fight on a regular basis. So she set out to follow them, starting with Rundas on the planet Bryyo. An ice-wielder going to a fiery world was not a good idea in Samus’ mind.

And as she predicted, Rundas was already in deep trouble. Samus could sense that Rundas was feeling pain and agony-somehow she could sense it. Was it the phazon, or was it something else that allowed Samus to sense that her friend was in danger? Samus hoped that her senses were fooling her, but when she met Rundas, it was obvious that what she sensed was real. Rundas appeared, opening fire on Samus, babbling about how the “great one” has made him open his eyes to the truth-that he and the other phazon-infected life forms were superior to their non-infected counterparts. He was exhibiting no sense of self-preservation or sanity. The Rundas that Samus knew was gone.

Fighting despite the odds, Samus defeated Rundas. In one last moment of clarity, Rundas reached out for Samus,. Asking for her help in fighting the corruption in his mind. But then he was killed by getting impaled on one of his own icicles. Samus watched as Rundas died right in front of her, with Dark Samus taking his corpse. Samus was distraught at the sight. Unable to look at the sight, Samus then headed for the phazon seed that was on the planet, and destroyed it. She fought a massive Bryyo mechanoid, only to destroy it and move on.

Samus then moved on to the gas giant, Elysia, where Ghor had gone. Her thoughts about her remaining friends were calmed as she beheld the beautiful gas clouds that surrounded the installation. As she explored the place, however, her ship came under attack and she knew who it was. Ghor, like Rundas, had been rendered mad by the phazon and Dark Samus. Ghor was now a vicious marauder, using his machine to attack Samus as she got to his location. Samus tried to reason with Ghor, but as with Rundas, there was no-one to reason with. Ghor was not listening. Samus was once again forced to fight another old friend. Ghor took control of the local space pirate forces, which perplexed Samus-these infested former colleagues of hers were in-sync with the space pirates. Was Dark Samus coordinating with them as well?

After another pointless and tragic battle, Ghor was felled by Samus’ superior firepower. Ghor tried to transform into a gunship, but his armor exploded and he was left adrift, with Dark Samus once again reappearing to collect a fallen pawn. Samus was beginning to get tired of that sight. Samus’ ship received an emergency transmission from an unidentified Federation soldier who transmitted the coordinates of a space pirate world. Admiral Dane confided to Samus that Gandrayda was searching that sector. Fearing the worst, Samus headed there right away. Gandrayda was the most delicate among her friends, and Samus feared for her life. As she fought her way through space pirate forces and traps, she began to read through their journals, and she discovered a horrible truth.

Dark Samus had taken control of them. After kicking them around back on Aether, Dark Samus found a way to take control of them, and she killed those who disobeyed. Her new followers obeyed her with near-religious zeal, and her control of them was absolute and unquestioned. Even Ridley followed her now. Samus fought her way through and found the soldier that transmitted the location. She asked for Gandrayda, but the soldier said that he knew nothing. But as they walked across the pirate base, Samus walked into a trap. The soldier was no soldier at all: it was Gandrayda, who disguised herself with her powers. Samus’ worst fears came to pass: Gandrayda was infected, and she had gone mad. Now Samus had to fight her comrade once again, all thanks to Dark Samus’ corruption.

Samus once again tried to hold back, tried to take her target alive, but alas, as they fought, Gandrayda sank even deeper into madness. She used many different combat forms, including those of Ghor, Rundas, and Samus herself. But still, Samus proved to be the superior fighter, and once Gandrayda was hurt enough, her powers went haywire, and Samus was once again treated to the sight of a comrade dying before her eyes as Gandrayda transformed uncontrollably, finally turning into an image of Samus asking for help before she perished. Once again, a wraith of Dark Samus came about, and absorbed Gandrayda’s remains. Samus, now with white-hot fury, opened fire on Dark Samus, to no avail, screaming “GIVE HER BACK!” But Dark Samus just withered and disappeared, unaffected by Samus’ raging.

Admiral Dane and a small strike force followed Samus as she angrily plowed through the space pirate defenses, and he came upon that sorry sight of Samus raging, screaming, and shooting the remains of the space pirates in a fury, she fell into a sobbing wreck, distraught over the losses of her friends, asking if loss was the price for love. Her real family was gone. Her adoptive parents were gone. And now, her friends were all but dead. All the admiral could do was hug and console Samus, as her losses drove her to sorrow. Castor reasoned to Samus that this was the life they all signed up for when they took up arms to defend the innocent-death is something one has to accept when one fights. That was an inescapable part of life. Samus recovered from her despair, and prepared for the assault on the greater enemy fortress that laid before them.

Samus fought her way through more space pirates, her heart full of sorrow and anger. She no longer cared about self-preservation, and she sought to kill any enemy in her way. “No mercy” she thought. “No mercy for this scum.” Dark Samus was another product of these space pirates tampering with nature, and the war Samus fought now was no different from the one she was fighting throughout her whole life. She once again fought Ridley, and with her rage, she crushed him easily. After defeating him, she destroyed another phazon seed. But with each seed she destroys, her health becomes worse as the seeds’ explosions increased her phazon level. Slow by slow, she was losing her humanity, and her rage was exacerbating the problem, as her rage made her new phazon powers more potent.

Samus’ body began to revolt, as she threw up after the phazon increased made her feel sick. Samus rested in her ship for a while, then got back on the job. After looting a derelict frigate for the coordinates of the phazon homeworld, Samus joined Dane’s fleet for a final assault at the place, but as ships fought above the world of Phaaze, Samus landed with only one goal in mind: killing Dark Samus and destroying the planet. As she landed, her phazon condition got worse, as she walked on the ground, her own ship no longer identified her as a human. She trekked on through nonetheless, resolute in killing Dark Samus. Once she met Dark Samus, she engaged her and the battle began. But even Dark Samus’ might was no match for the grieving Samus. She lost no matter what she threw at Samus. Multiple duplicates of herself, and even fusing with the Aurora unit present there. They were of no avail. The battle was over, and the planet shook to the core, since the Aurora unit was linked to the planet core, which now went volatile.

Samus’ phazon condition was cured from a shockwave caused by the death of Dark Samus. Samus then jumped back to her ship, which now recognized her as a human. As the planet fell apart, Samus got away and flew past Dane’s fleet. The battle was over, but Samus preferred solace rather than celebration due to the loss of her friends. As Dane’s fleet was filled with men cheering the destruction of Phaaze and the phazon threat, Samus’ ship flew away, with resting in her bed alone, grieving for her lost friends as she stared into the empty void of space.

OTHER M STORYLINE

Some time later, Samus came around another ship, and once again, fought Ridley over a Metroid. She later landed on Zebes, where once again, she fought against Ridley, Kraid, and Mother Brain. This time, she finished off Mother Brain with the help of a baby metroid that saw her as its mother. After that battle, she once again woke up in a Federation installation where they inspected her and received her account of what happened on Zebes. Zebes was destroyed due to a chain reaction in the pirate base causing the planet to blow up, but now, it seemed that Mother Brain would trouble them no more, for she saw to its death personally.

If only that were the truth…….

The Federation managed to nick genetic samples from Samus’ armor-samples that included the metroids, the Zebesian space pirates, Ridley, and even Mother Brain. They commissioned a science team to work inside a garden environment sealed inside a bottle ship where research on these new subjects being cloned commenced. And not only did they clone Ridley and the space pirates, they cloned some metroids as well, and created their own “Mother Brain.” A humanoid cyborg named MB was left to a bunch of scientists to grow. They thought that a human interface would be easier to manipulate rather than an alien one. And so, they went with their experiments, unaware of the consequences of playing God.

The head scientist in the bottle ship, Dr. Madeline Berman, allowed MB to believe she was her daughter, Melissa Berman. But once “Melissa” started exhibiting thoughts and feelings outside the set of limits and parameters that the Federation devised, they decided to pull the plug on the experiment and tried to terminate “Melissa.” To their horror, “Melissa” showed that not only can she control the nearby metroids, but she could also control the Zebesian space pirate clones as well, and she used them to purge the facility and kill almost everyone but Madeline, who sent out a distress signal. And ironically, Samus was one of those who received the signal and responded to her. However, once again, she was not alone.

Samus responded to the call, but as she wandered around the so-called “Bottle Ship”, she met up with a familiar face: General Adam Malkovich, her old CO in the Galactic Federation Military. Adam was surprised to see Samus as well, and the two of them fought a monster together along with Adam’s unit before the two got to talking. Samus respected Adam, but gave him the cold shoulder. After the loss of her hunter friends, she did not want more losses, and as such, recommended to Adam that he and his men go home. One of Adam’s men, an old friend of Samus by the name of Anthony Higgins, tried to make friendly small-talk with Samus, but he got back no response.

Adam then reminded Samus that survivors may be nearby, and advised against the use of her more powerful weapons and gear. Samus then responded that such a stipulation would cost him extra if he wants her to help. To ensure Samus’ obedience, Adam paid her up-front, paying her half the promised amount, and he told her that the other half would be given once the mission was complete. Samus agreed, and she submitted to Adam restricting her weapons.

Samus and Adam’s team explored the ship, and so, Samus came across the space pirate clones-wearing Federation badges. She came across a creature resembling Ridley, but with fur and no wings. As she explored more of the station, she came across Ridley. Ridley emitted a high-pitch scream that scrambled Samus’ mind, and memories of her family’s death came flooding right back. Her anger began to boil, and she charged and savaged Ridley just as Ridley was about to kill Anthony. Samus was one step away from killing Ridley again, but both Anthony and Adam advised against it, preferring to interrogate him instead. Samus was dead-set on killing Ridley, wanting to send him “back to hell where he belongs,” but she relented at the last moment, allowing Adam to take the battered beast to their makeshift HQ in the ship.

Another problem emerged when Samus met up with Melissa Bergman, who identified herself as Madeline. Samus thought she was a survivor from the science team, but she was reluctant to deal with th Federation, as she told Samus how she saw a Federation soldier gun down another. Samus reported this to Adam, but Adam couldn’t contact the rest of the team for proof due to some sort of communications block. What’s worse was that this “deleter” attacked Samus with some construction machinery, then when Samus tried to ensure Melissa’s safety, the man was gone. Samus also lost the girl, and was once again left to wander around the ship like a ghost, looking for survivors or the traitor.

Ridley managed to escape the Fed troopers and steals a ship to escape, but now, Samus ran across the real Madeline Bergman, who then explained that the girl she met was an android copy of Mother Brain that went mad due to the Federation attempting to shut her down. They were beset upon by a Queen Metroid as the Bottle Ship went into FTL, ready to crash onto the Federation capital. After dealing with the Queen Metroid, Samus bumped into Adam, and Samus proceeded to lock Adam and Anthony at the safety area with Madeline as she left to fight “Melissa”.

But she wasn’t alone. A second group of Federation soldiers apparently snuck in before the ship jumped. They arrived to engage Melissa, only to nearly get slaughtered by another group of monsters. Samus manages to land a shot at Melissa, and disables her. Samus then stopped the ship from crashing by deactivating the FTL drive with the navigation computer nearby. The Federation troops prepared to kill Melissa Bergman. As she braced for the worst, Samus decided to shield her because she was just a girl driven mad by Federation experiments. The colonel commanding the troops ordered Samus to leave, but she chose not to. The colonel threatened to arrest Samus and have her contract with the Federation terminated, but Samus stood her ground.

The stalemate ended with General Adam Malkovich ordering the colonel and his troops to stand down. He and Anthony gave credence to Samus’ story and prevented the Federation soldiers from killing her. They then had MB sent to an asylum institution made for gifted children where Madeline can watch over her. Samus then left the ship after Adam paid her the other half of the money she was promised for doing the job. She then fully expressed to him that she loved and cared for him and Anthony, but she didn’t want him to share the fate of her family and friends. Samus stayed on the Bottle Ship to help clean it of monsters, and after encountering and defeating another monster, Phantoon, she recovered some old files that Adam left behind along with his helmet. She escaped the Bottle Ship as it was beset by Federation cruisers opening fire, getting away in time as the Bottle Ship was incinerated in space.

METROID PRIME: ARMAGEDDON

Samus thought that the worst had come and gone, but she was horribly wrong. A figure who looked like Samus attacked a Federation shipyard, killing thousands and leaving few survivors. It happened again, with another shipyard falling to this figure. At the same time, Samus continued to get visions and dreams where she killed whole space stations’ worth of people, and the government naturally suspected that she was behind those incidents. Several powerful Federation officials who didn’t like having this independent-minded bounty hunter interfering in Federation business used the attacks as an opportunity to get rid of her once and for all. Against the advice of Admiral Dane and General Malkovich, who suspected that an impostor was behind such incidents, the Federation dispatched a task force to apprehend Samus, and the young bounty hunter was forced to flee her former employers and was now on the run, with her ship fleeing civilized space as Federation fleets and other bounty hunters began searching for her.

As Samus fled from her former employers, the Zebesian space pirates under Ridley were back in action, sacking planets and space stations left and right. Residual effects from both the Samus attacks and the pirate attacks pointed to one thing in common: phazon. The threat that was once thought of as extinct once again reared its ugly head, threatening the galaxy with its horrible power. And as if this was not enough, the Kriken Empire, an enemy of the Galactic Federation, also emerged as a threat. The red-skinned insectoid invaders were feared by the Federation, but it seems that now, they’ve become more aggressive than before, with one Kriken fleet cornering and destroying a Federation fleet right after it was dealing with a space pirate attack on a nearby shipyard.

Samus would have assisted, but with a bounty on her own head, she could not help. The Federation forces were hunting her as much as it did the space pirates or the Kriken Empire. What made these attacks different was how precise they were. The space pirates were no longer fighting like a rag-tag pirate band, they were more like a professional outfit of shock troops hitting the Federation at its weak spots. They once fought like bandits stealing and scavenging here and there on undefended worlds, but now, their attacks had pinpoint accuracy, striking at Federation shipyards and disappearing before Federal reinforcements arrived.

Similarly, the Kriken fleets seemed to always strike when the Federation forces least expected it, right after they fought off space pirates. The Kriken fleet seemed to follow up the space pirate attacks, as when the Federation fleet deploys to hunt down space pirate bases, the Kriken ships catch them flat-footed and unaware. And as with any battle, “surprised” became another word for “dead”, as one ambush after another led to Federation forces getting massacred on many fronts. It got so bad that the Federation forces retreated to the galactic core: they no longer responded to space pirate attacks on outlying shipyards or colonies, out of fear for a Kriken ambush. This then left many outlying colonies unprotected as the Federation abandoned them to the space pirates and the Kriken, with both getting stronger as they looted more resources to fund extra campaigns.

This was far worse than anything the Federation had faced up to that point. For far too long, they have become complacent, dealing with minor threats like piracy. Not since the Bacterion and the Belsar did the Federation face such rabid foes. But even as the Federation was collapsing, even as member states left for fear of space pirate and Kriken assaults, they still tried to hunt Samus down, blaming her for the attacks and proclaiming her either a traitor or a brainwashed stooge controlled by the enemy. The truth was far more sinister: Dark Samus was the leader of the space pirate attacks, and she coordinated them with help from the Kriken Empire. She survived the destruction of Phaaze thanks to Federation scientists retrieving some of her remains to be used as a power source. Instead of finishing her off, these Federation scientists unwittingly revived her, and she broke free of their control after killing off the scientists.

If the truth was ever to come out, the failing Federation government would lose the small shred of credibility it had left. This might even lead to the collapse of the Federation as they knew it. So, to save face, they continued to point at Samus, insisting that she might have turned traitor or the space pirates might have captured and brainwashed her. Military assaults, the Federation can withstand. Losing the trust of the people? Not so much. As Samus continued to try and escape the Federation, she came upon a space colony under attack. Ever the heroine, Samus couldn’t stay away-she went in to help, only to get captured once the Federation forces showed up. Luckily for her, however, the Federation forces that caught her were those of General Adam Malkovich and Admiral Castor Dane.

Dane argued that perhaps Samus wasn’t to blame. Perhaps the space pirates cloned her and created a copy of her armor. Perhaps Dark Samus survived and she was taking her revenge. But, according to Samus’ past accounts, Dark Samus was dead, so Malkovich argued that Samus was captured by the space pirates or infected by some phazon creature, and the dreams she gets are her flashbacks of being forced to serve them. Adam then had Samus stripped of her armor and put in containment so as to keep her from harming others or herself. Samus, confused due to her dreams and doubting her own sanity, allowed herself to be placed in quarantine and falls asleep in her restraints as she’s left in a Feddie installation while Dane and Malkovich went back to waging war.

Then the lights went out and Dark Samus appeared. She appeared not in a suit of armor, but as a dark mirror of Samus the woman, complete with dark blue skin and a dark blue phazon Zero-suit. Dark Samus taunted her counterpart, saying that the world will always throw her under the bus if the need suits them. Samus struggled in her bonds, but she was helpless as Dark Samus whispered into her ear. Dark Samus states the obvious-that she can easily kill Samus right now. But she isn’t here to kill, but rather, to give her progenitor-her “mother”, an offer. There was nobody in the galaxy like the two of them, Dark Samus said. There was nothing that can stand in their way if they worked together. All Samus has to do is to give in, and allow the phazon to guide her. She no longer needs to suffer the idiots of the Federation or clean up after the space pirates. If they worked together, they can rule the galaxy. Then nothing will ever hurt them ever again.

Samus seemed to let her guard down. The offer was intriguing, she said. Dark Samus then tells her that despite the bad blood between them, Samus still created her, albeit accidentally. The two of them still share similar traits, and together, they would be unrivaled. But as Samus said yes, and as Dark Samus began to unlock her shackles, Samus’ body was communicating one idea while her mind had another. When her hand became free, she struck at Dark Samus with a fist, and then she proceeded to unlock her shackles with her free right hand. She was free. Furious at Samus’ betrayal of trust, Dark Samus threatened to make her death agonizing, only for Samus to hit the alarm which called soldiers to their location. Dark Samus disappeared before the Federation troops can spot her. Samus knocked down some of the troopers, stealing a freeze ray from one of them and pinning Federation soldiers to the wall with ice blasts until she managed to get back her power armor and ship, blasting her way out of the station.

Samus then spotted Dark Samus’ ship and attacked her when she was attacking another Federation fleet with Admiral Dane on it. Seeing the proof that Samus was not with the space pirates, and seeing how Samus and Dark Samus were fighting each other, Admiral Dane and General Malkovich lent a hand, driving Dark Samus away. But it was all a feint. The bulk of the Kriken and space pirate fleets appeared, attacking the Federation capital while the fleets were busy guarding the borders of the core worlds. They annihilated the Federation’s home defense fleet and invaded the capital city, killing billions in their rampage through both orbital bombardment and ground invasion. Dane’s fleet arrived just in time with Samus and Adam, and the final battle began. While Adam led the ground assault, Dane led the fleet, and with the space pirates the Kriken feeling cocky after destroying the Federation capital’s home fleet, Dane was able to lull them into a false sense of security, with his cloaked vessels attacking from behind while his regular ships put full-power to their front batteries, hitting the enemy with a surprise attack and devastating the enemy fleet.

The city was still in flames, and Samus rode out to meet her personal foe in combat. She once again fought against Ridley, but before she can finish off the reptilian pirate, Dark Samus arrived. Samus diverted her attention to her dark counterpart, and the final battle of the war began. This time, Dark Samus was more powerful than ever before, thanks to her feeding off of her followers and devouring other life forms with phazon. However, Samus countered that by bringing her best suit-a suit of light energy from Aether designed to counter phazon. Samus countered her dark counterpart’s blows and before long, Samus went on the offensive. As Dark Samus tried to throw all sorts of attacks at Samus, from phazon blasts to massive beam attacks, Samus countered back with her own attacks, and just like on the planet Phaaze, Dark Samus began to lose. Before long, Samus landed a fatal blow to her dark counterpart by mixing her own beam weapons with the power of her suit’s light energy, further weakening Dark Samus’ regenerative capabilities, as well as her control over her own powers. As Dark Samus was getting crushed by the weight of her own dark powers, she exploded, and as for what happened next, Samus couldn’t believe her own eyes.

Ghor, Rundas, and Gandrayda materialized from the raw phazon energy that was released from Dark Samus’ demise. When Samus asked how this could be possible, Gandrayda explained that their consciousness remained within Dark Samus, and when she died, they took their opportunity and seized bits and pieces of her power to materialize themselves once more. They were now alive, and perfectly sane as well. Rundas yelled out “the nightmare is over!” and they all hugged together. Samus was overjoyed at the return of her old friends, and together, they celebrated their victory over Dark Samus.

As the remnants of the invaders were getting annihilated by Dane and Malkovich’s forces, their Federation troops herded the Federation leaders towards Samus, to whom they apologized to, for framing her for Dark Samus’ attacks. Samus accepted the apology, although she had her own private doubts that these leaders learned nothing from their mistake and might try another foolhardy experiment down the line. The Federation army then gave Samus a victory reception, with the troops lined across the streets saluting her. Dane and Adam asked Samus to join them and take a spot as a Federation general. Samus declined, saying that she was a bounty hunter to the end, and that she will always be one. Samus marched to her ship as the soldiers saluted her, with her friends in tow. She got onboard her ship with her friends, and they flew off into the stars.

After a night of partying with her friends at their favorite bar, her friends went on their own separate ways, each going off after bidding Samus farewell. However, as she slept back in her ship, the only thing Samus could think of was Dark Samus. She couldn’t shake the feeling that Dark Samus was still alive. She went to the restroom, washed her face, and suddenly, she saw Dark Samus’ left hand on her own. Then, she heard Dark Samus’ chilling voice in her mind: “YOU WILL NEVER ESCAPE ME!” The vision faded, and Samus looked at her left hand, which was normal once again. Was it a mere nightmare, a figment of her imagination? Or was it something more sinister than she could possibly imagine? Only time will tell.

MOTHER BRAIN AND THE AWAKENING OF PHAZON SAMUS

Despite the fact that Samus defeated the original Mother Brain back on the planet Zebes, she did not die. In fact, she managed to survive and construct for herself a new body after escaping the destruction of Zebes. She regained contact with Ridley, the space pirates, and even the remnants of the Kriken invasion fleet that was limping back home after its defeat at the hands of Samus Aran and the Federation. It was a trifling matter for the Chozo Supercomputer to tempt these wayward rejects and outcasts to take revenge on the woman who wronged them the most-Samus Aran. Mother Brain and the Zebesian Space Pirates convinced the Kriken that they were all after the same prey, and they added what remained of their forces to hers and the Space Pirates.

To aid in this quest of vengeance, Mother Brain hired several other bounty hunters-aside from Trace who was part of the Kriken forces, she hired Sylux, Weavel, and “Big Time” Brannigan. Weavel and Sylux harbored a strong hatred for the Galactic Federation in general and Samus in particular, and they even joined in on the Space Pirate raids during Dark Samus’ reign of terror, only for it to be cut short when Dark Samus fell in battle in the Federation’s capital. They also joined in because Mother Brain put in a high enlistment fee due to her hacking several Galactic Federation bank accounts and transferring the wealth to a private account owned by her. Brannigan joined out of pride, wanting to be known as the one who took down Samus Aran, since his own efficiency rating was 100%, and he has never failed to bring in a bounty.

Unlike the previous engagements where the Space Pirates and the Kriken would either bunker down at a station until they get attacked by Samus or they attack a Federation stronghold or ship en-masse, this time, Mother Brain opted to stalk her prey. Ridley and the others were ordered to hold back while the likes of Brannigan, Weavel, and Sylux kept their eyes on Samus and stalked her as she went from place to place, looking for a chance to capture her. Mother Brain eventually hit upon a trap she knew Samus would not be able to resist.

Mother Brain found a remote jungle planet with Chozo ruins, and had her forces garrison a derelict Chozo temple there to lay wait in ambush. To lure Samus there, Mother Brain sent out a false Chozo signal using a Chozo beacon, a transmission that spoke of hidden weapons and upgrades to power armor hidden inside a special temple. Always looking to upgrade her weapons and armor, Samus came to the planet, and as she headed for the temple, Sylux, Weavel, and Brannigan trailed her, while an entire Kriken army as well as Ridley’s Zebesians were waiting in ambush. When Samus got inside the temple, she found nothing but the Chozo beacon, and as she looked around for the upgrade for her Chozo battlesuit, explosives set up at the foundations of the temple were detonated and the ruins collapsed on top of Samus. Protected by her battlesuit, Samus was unaffected by the rubble crashing on top of her, but as she burst forth from the ruins, Brannigan, Sylux and Weavel attacked. Each one of them would have posed a significant threat to Samus on their own, but all three of them attacking kept her on the defensive and barely able to land a hit. As they pelted her with energy blasts and missiles, she kept trying to look for higher ground, and she managed to use higher ground against them to blast them with missiles and blow them away, and they fell down from the mountains.

But as she retreated to the mountains, Ridley caught her by surprise and attacked. Already tired out from fighting the other three hunters, Samus was unable to defeat Ridley this time, and it was a draw. Then the rest of the Zebesians and Kriken soldiers turned up, mass-firing at Samus as she fled the mountain and into a jungle. Some of the Zebesian and Kriken troops were also in said jungle, and Samus found herself surrounded by enemies as Ridley bombarded her from the sky with fire breath while the other enemy troops kept her pinned behind trees lest she get perforated by several hundred Zebesians and Kriken troops taking potshots at her. Even the other hunters that she evaded before showed up to join in. Finally, Samus decided to make a beeline for her ship to get away, only for her to get two shots in the legs by Trace and his sniper weapon, the Imperialist. The beam weapon penetrated the weakening armor and injured both of Samus’ legs, making her unable to run as Ridley, the Zebesians, and the Kriken swarmed her.

Samus awoke to see herself chained in a healing tank. The juices of the tank healed her leg wounds, but she was half-naked and defenseless, with no armor, no weapons, and barely any clothes to cover herself. As she awoke, the healing fluids were drained from the tank. Mother Brain taunted her. “This is the great hero that saved the galaxy? The one who crushed the Zebesians and the Kriken as they were but one step away from victory?” As Samus struggled in her chains, Mother Brain laughed at how helpless Samus was. The great Samus Aran, destroyer of worlds, annihilator of pirates, savior of the galaxy......now half-naked and chained like an animal in a petting zoo. As Mother Brain laughed, the other pirates, Kriken, and hunters laughed too. Weavel mocked Samus and told her that this was restitution for her injuring him and killing other Space Pirates. Sylux mocked Samus and asked “Where is your Federation now?” Brannigan boasted that with Samus out of the picture, he would become the best bounty hunter in the galaxy. Trace told Samus that the Kriken send their regards in response to her stopping them from taking over the galaxy. Ridley joined in on the mockery, telling Samus that despite all her accomplishments, despite all the honors the galaxy pours upon her, without her weapons, she was nothing, just a scared, whimpering girl, like how she was when he killed her parents before her very own eyes.

When Samus spat back, saying that they should just end it all now and kill her, Mother Brain stated that she was far more useful alive than dead. Her scanning of Samus’ body while the latter was unconscious showed that she still had phazon in her body, albeit in a suppressed state. Apparently, Dark Samus’ explosive death during the battle at the Federation capital left its physical mark on Samus, and her body is once again slowly cultivating its own phazon supply. Mother Brain theorized that when exposed to the right stimuli, her body can once again be a phazon factory, and once that happens, she will be trapped in a terrible existence between life and death, her power feeding them as they conquer the galaxy! When Samus spat back, saying that she’d rather die than live as their slave, they gagged her and pumped liquids back into her tank, and forced her to watch as they injected her with serum after serum. Soon, she felt the familiar rush of phazon in her body, and as her body produced more and more phazon, the more they pumped it out of her. With the destruction of Phaaze and Dark Samus, she was now their top phazon source, a living oil well that gave them more of that power source. Mother Brain assured her that she will be kept in a healthy condition, only so they can pump more phazon out of her body to power an entire army. The juices of the tank and the serums they pump into her would make sure that she has more than enough nutrients coming into her body, which would allow them to keep pumping out more phazon from her.

Listening in on Mother Brain’s speeches to her troops, Samus pieced together their plans: according to Mother Brain, the “mistake” that Dark Samus made was that she was too hasty in attacking the Federation. She didn’t fully utilize the power of phazon. With all the phazon that they were pumping out of Samus, they will have more than enough to empower every single Zebesian and Kriken soldier in their army, and the same goes true for Ridley and the other bounty hunters in Mother Brain’s employ. Similarly, Mother Brain found several cloning devices from other Federation space stations that Ridley looted while Samus was being pumped like an oil well, which will allow them to recoup their manpower losses after Dark Samus’ abortive attempt at invading the Federation capital. There were also many resource-rich nodes that they can mine for materials to make more warships and shipyards that Ridley targeted for conquest, far away from the prying eyes of Federation authorities. With the Federation busy funding reconstruction projects after the last war, they didn’t have enough to fund the rebuilding of the Federation fleets. Once Mother Brain and her forces have rebuilt their armies and fleets, the Galactic Federation will be their target once more. This time, there will be no Samus to stop them, and they will show the galaxy the full power of phazon. Dark Samus would have won had it not been for Samus distracting her and keeping her attention. Now, with a new leader who has Samus under lock and key, they have a common purpose. One leader, with one army, and one purpose, and no hero to stop them.

Samus could barely hold back her contempt and anger. Here she was, powerless and without strength, trapped in a glass tank, being pumped for phazon that is now feeding her enemies’ strength, unable to even speak, so much as move around. No matter how she tried to remain calm and try to find a way out, the rush of phazon and the effects of the serums that she was being pumped with had their toll. She was angry. She sought revenge. She wanted a way to strike back. To strike back at Mother Brain, who betrayed and murdered her adoptive Chozo parents. To strike back at Ridley, the being responsible for the death of her real parents. To stop this doomsday plot before it even starts. But the more she struggled against her chains, the more they pumped her with serums that drained her strength and made her fall asleep. There was no rescue, nobody was coming for her.

Samus began to think that she really should have taken up Castor Dane and Adam Malkovich’s offer to make her a Federation general. At least the Feds would have become rather suspicious at the loss of one of their generals and would have sent in an army to rescue her. But with her being an independent bounty hunter, her disappearance wouldn’t concern them. They probably think that she was off hunting down pirates or criminals on her own, or looking for some alien artifacts. But no. She was trapped in this hell, with her enemies jeering and smiling at her fate as she struggled against her fate. This continued on for weeks on end, until suddenly, one day, a voice spoke from within her mind.

"Let me out," the voice said. "Let me out, and together we can CRUSH THEM!"

Samus knew that voice.......it was the voice of Dark Samus.

"NO!" Samus thought. "The last thing I’d do is let you out! I’d rather die!"

The voice mockingly answered back: "If you don’t let me out, then we won’t die, but the Federation will. We both know what Mother Brain is like. She won’t stop at merely conquering the capital of the Federation. She will only stop until everything is hers."

"YOU TOOK MY FRIENDS!" Samus responded. "YOU HURT THOSE I LOVED! LESS THAN A MONTH AGO, YOU KILLED TRILLIONS IN YOUR WAR! IF I LET YOU OUT, YOU’LL DO IT ALL OVER AGAIN!"

"Yes, I did all of that." The dark voice responded in a blunt tone. "But now, ever since I 'died', I have been living inside you. We are one now, whether you like it or not. Your thoughts are my thoughts. Your fears are my fears. If we don’t work together, YOU will continue to suffer. I will continue to suffer. I’d rather not live out the rest of my days as a cross between a trophy and a crude source of power. Wouldn’t you like to stop them before they destroy everything you loved? If you don’t accept my help, if you don’t surrender to me, then trillions more will die. Are you willing to let them all die based on your pride?"

"How can I trust you?" Samus asked. "How do I know you won’t turn around and kill everyone through me?"

"Because you’re in control, Sammy." Dark Samus’ voice responded. "If I could take your free will away, you’d be gone by now, and I’d be in full control. But if we work in sync, if we work with our minds in tandem, there is nothing that can stand in our way! Not Mother Brain, not Ridley, not the other hunters, the Zebesians, or the Kriken. We can crush them all and save your friends from a gruesome, nasty war before it can even start!"

Samus weighed her options. She can keep resisting the call of Dark Samus, but then she would remain here, trapped in this tank, chained like an animal, being pumped full of drugs, and being used as a phazon pump in return. If she accepts, she might be able to escape, but she isn’t confident enough with the idea that she can control that much phazon energy. She remembered back when she was using phazon in battle-there were times where she went full-aggressive against the enemy and when she felt the urge to kill nearly overpowering her sense of reason. But now, there was no other choice. Dark Samus was right. If Samus doesn’t accept her offer, then the Federation is doomed. It nearly collapsed from the last war. A second war with more powerful phazon-infused enemies led by a Chozo supercomputer would doom the Federation and usher in the kind of dark age that would surpass the reign of terror that the Bacterion and the Belsar had over the galaxy before they were vanquished.

Samus gave a heavy sigh, then surrendered herself to the rush of Phazon and her emotions.

"Yes, YES! Give yourself to me, let us be one!" The voice insider her said. "We will crush them with our might!"

Suddenly, the rush of Phazon in Samus’ body became too much to bear for the machine restraining her. The riding tide of phazon energy continued to expand until the machine pumping phazon out of her and pumping serums into her was blown away by a blast of phazon energy. She was free once more. Her body overflowed with the power of phazon, and the power created a suit around her body not unlike her regular power suit, complete with an arm cannon, except it was more like Dark Samus’ power suit than her old one. As Kriken and Zebesian elite troops with phazon devices came to try and return her to prison, they pumped themselves with phazon and opened fire at her-only to find their attacks being swatted away.

"You arrogant fools," she spat back. "Let me show you how a real master does it."

Samus charged up a mighty phazon blast with her arm cannon, and when it fired, it fired a massive beam of phazon energy that disintegrated her attackers. More and more Zebesian and Kriken troops came, and more of them died. They were no match for her. As the alarms sounded and the base went to full alert, the VIPs of the base, from the hunters, Ridley, and Mother Brain, were now alerted to what was going on-Samus, wrapped in the power of phazon, was casually annihilating their elite troops without so much as a scratch.

Mother Brain sent the other hunters after Samus, and their phazon-enhanced weapons and suits made them stronger than before. But Samus, with the power of phazon coursing through her veins, blasted them away as if they were ninepins in a bowling alley. Trace, Brannigan, Weavel, and Sylux were driven away easily, and they decided to escape the space station they were in rather than die at their posts. When Ridley came to confront Samus, he was terrified, as he witnessed Samus crushing the troops with ease and driving the other hunters away. Mother Brain then decided to confront Samus herself, with a phazon-powered mechanical body firing phazon beams at Samus. She had the strength, but she didn’t have the speed, as the newly-empowered Phazon Samus dodged her attacks and blasted her with a full-powered phazon blast. Mother Brain realized the utter terror she was in and fled. Samus continued her rampage until she came across a cloning chamber where Mother Brain was cloning more Zebesians and Kriken troops. Samus saw how a nearby computer was programming them for absolute loyalty towards Mother Brain, so she tampered with it and used the computer to program these troops to be loyal to the Federation instead. When they awoke, the clone troops destroyed their older brothers and seized control of the shipyard attached to the space station, taking control of nearby warships. With Mother Brain and her top lieutenants nowhere to be found, Samus and her clones found little opposition.

Surprisingly, Gandrayda, Rundas, and Ghor showed up. They were worried about Samus’ disappearance and decided to look for her, only to see a phazon-infused Samus wiping out Zebesians and Kriken while being backed up by her own army of Zebesian and Kriken clones. When Gandrayda contacted Samus, Samus told her that the Federation now has a new army programmed for absolute loyalty, and the Kriken and Zebesian ships being constructed at the shipyard was now theirs. Gandrayda and the others accepted it, but were worried about Samus. Samus powered down her phazon form and returned to normal-which put her companions at ease. Fifteen minutes later, Admiral Castor Dane’s fleet arrived along with General Adam Malkovich’s army, and Samus informed him of what happened-Mother Brain and her hired thugs captured her and tried to use her as a phazon source, only for her to escape and steal their army and fleet from under their noses. Dane congratulated Samus for her ingenuity, but Malkovich was nervous about how Samus was now using phazon liberally. However, they could not argue with the results: now the Federation has a way to make more soldiers, they now have more ships, and now, they have an enforcer for their regime who has powers that could send the fiercest warriors in the galaxy running with their tails between their legs. Samus retook her armor and ship, and flew back to the Federation capital with her friends and her newly-acquired army and fleet, with Dane’s fleet in tow. Apparently, there was a matter that the Federation government wanted to address.

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