Samus Aran/Synopsis

The synopsis of Samus Aran from the series.
==Early Life==
Samus was born to Rodney and Virginia Aran on the Earth colony K2-L. She lived happily with her parents until she was three, then the colony was raided by the Space Pirates and their commander, Ridley. They ravaged the colony, killing Virginia, who protected Samus from Ridley in her final moments, along with every colonist there, except Samus, while Rodney detonated the Afloralite reserves that the Pirates had stolen at the cost of his own life. The encounter traumatized her deeply as she lost her parents and her home in a single blow. After K2-L was destroyed, Samus was adopted by the mysterious Chozo race, who took her to Planet Zebes to raise her after arriving just in time to save her from the Pirates and Ridley when they got the colony's distress signal. After being adopted by the Chozo, she was infused with their DNA to help her survive the harsh environment of Zebes, and trained by them over the years to become a formidable warrior. 
After that, she returned to the Galactic Federation to enlist in the Federation Police, serving under Adam Malkovich, before deciding to become a bounty hunter, though still accepting any jobs that the Federation had available for her.
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Samus is assigned to head to Planet Zebes to eliminate the Metroids living on the planet, along with the Space Pirates' AI, Mother Brain. After dealing with Kraid, she later has to deal with the Space Pirates' commander, Ridley, when he arrives on the Space Pirate Mothership to the planet. Once she defeats Ridley, she is granted access to Mother Brain's inner sanctum. After critically damaging Mother Brain, triggering a self-destruct sequence, she escapes back to her gunship and tries to flee the planet, but no sooner after she powers down her Varia Suit, her ship is surrounded by Space Pirate fighters and is damaged, sending it crashing back to Planet Zebes. Samus survives, but with her ship and Varia Suit destroyed, and armed only with her Zero Suit and Paralyzer pistol, she's forced to carefully navigate her way through the Space Pirate Mothership until reaching some Chozo ruins, where after passing a test the Chozo had left for her there, she's granted what would become her trademark Power Suit for the majority of the Metroid series. Infiltrating the Space Pirate Mothership again, Samus defeats Mecha Ridley (a robotic weapon made in Ridley's image) which triggers the ship auto-destruct sequence. Fleeing to the hangar, she commandeers a Space Pirate fighter to make her escape from the Mothership and Planet Zebes just in time before the Mothership is destroyed.
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Samus responds to a distress call from a Space Pirate frigate over the planet Tallon IV. Arriving on the frigate "Orpheon", she finds most of the pirates dead from parasites that infested the ship. Dealing with the Parasite Queen in the reactor chamber, the Queen ends up falling into the ship's reactor and setting off a chain reaction that threatens the entire ship. Samus attempts to evacuate, but one explosion stuns her and causes many of her Power Suit's abilities to be damaged. She also has a brief encounter with Ridley, who has been reconstructed has a cyborg called Meta Ridley, before she manages to escape the frigate and soon heads down to the surface of Tallon IV. While exploring the planet, Samus discovered that it was once a home to the Chozo and that the environment had been exposed to an alien material called Phazon. She makes her way through the various regions of the planet, dealing with the Space Pirates, other wildlife, Chozo ghosts, and bosses that defended many of her abilities and then some. She eventually regained the abilities that were disabled back on the "Orpheon", along with acquiring the Gravity Suit, Wave Beam, Ice Beam, Plasma Beam, and their Charge Combos which were powerful modes that were similar to the Super Missiles for her standard Power Beam, such as the Wavebuster for the Wave Beam, Ice Spreader for the Ice Beam, and Flamethrower for the Plasma Beam. She soon defeats a powerful Space Pirate known as an Omega Pirate, in which the radioactive Phazon it carried powers up Samus' Power Suit into the Phazon Suit, a black, grey, and red version of her Power Suit that protected her from all the dangerous blue Phazon she had found around Tallon IV. After collecting 12 Chozo Artifacts and taking them to the Impact Crater, where the planet's flow of Phazon originated from, Samus gets into a confrontation with Meta Ridley before she is able to descend into the depths of the mysterious meteor. She fights her way pass the deadlier red Phazon and Fission Metroids until she found the source of the Phazon that had contaminated Tallon IV, Metroid Prime.
After fighting its armored carapace through several areas where it could only be damaged by one of her Arm Cannon's weapons at any single time, be it the standard Power Beam, Wave Beam, Ice Beam, or Plasma Beam and its Charge Combo move, she then fought its true form when it emerged from its armored carapace. Using the pools of pure Phazon it spawned to power up her Arm Cannon to use the powerful Phazon Beam against it, it seemed that Samus was able to defeat it, but in a final move, Metroid Prime tried to assimilate Samus as it impaled a tentacle into her and tried to drag her into its surviving blob of Metroid nuclei and Phazon, but after some effort, Samus broke free, but lost her Phazon Suit in the process, leaving her in just her Gravity Suit. She's forced to evacuate before the crater collapses and is picked up by her gunship. Taking off her helmet to survey the aftermath of the Impact Crater's collapse with her own eyes, she can only assume it is over before she descends back into her gunship and leaves Tallon IV.
Unknown to Samus, Metroid Prime lived, and used the Phazon Suit it took from her to craft a new identity for itself: Dark Samus.
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Some time passes since then, a telepathic message from the Tetra Galaxy, "The secret to ultimate power resides in the Alimbic Cluster." was sent out and the Galactic Federation caught on to this message and hired Samus to uncover the truth behind this message. However, several other bounty hunters have also caught on to the mysterious message and have motives of their own for searching for the "ultimate power". In order to achieve this, they must acquire eight Octoliths needed to power the Alimbic Cannon, which would permit access to the structure within another dimension named the Oubliette. Each of the Octoliths are under the supervision of the robotic Cretaphids and the Slenches.
In between various battles with various creatures and the hunters themselves, Samus found that the Alimbics, the former benevolent inhabitants of the Alimbic Cluster, has had a time of long-term peace and their society was prosperous until Gorea, a horrific monster appeared in the form of a comet and drove the civilization into chaos. With no other choice, the Alimbics have gave up their lives to imprison Gorea inside the Seal Sphere which is kept within the Oubliette and left behind a cryptic prophesy on how Gorea can be defeated for good.
Once all eight Octoliths and making use of them to activate the Omega Cannon, and Samus and the other hunters rushed to the now accessable Oubliette. The other hunters beat her to it and come across an immobile structure and without a second thought, they opened fire against it, believing that it contained the ultimate power. To their shock, Gorea emerged from the Seal Sphere instead. Samus arrived on time where she bears witness to Gorea using its gigantic tentacles to deprive the hunters of their powers and the hunters disappeared, with only Samus left to face off against it. She first activated the panels stationed around the arena as the Alimbic prophesy stated and exploited its connection to the Seal Sphere. As Gorea reveals its true and final form to continue its attack. Fortunately for Samus, she is able to gain access to the Omega Cannon, which she uses to shoot Gorea's second form, causing both Gorea and the Oubliette to explode. Samus and various other hunters managed to escape with their lives intact. Once Samus is within the safety of space, she receives a vision of the Alimbic spirits appearing to thank her for her efforts.
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Samus is assigned by the Galactic Federation to investigate the loss of contact with the GFS Tyr, which was investigating the planet Aether and pursuing a Space Pirate frigate it crippled in battle over the planet when contact was lost with its contingent of Federation Marines. When Samus approaches the planet, her gunship is caught in a terrible storm and crippled by lightning, forcing her to land to effect repairs. While her gunship recovers, she investigates the compound the Marines had set up and finds video footage showing them having been attacked by unknown hostiles and completely wiped out. Further investigation causes her to find a portal that leads to a parallel version of Aether known as "Dark Aether". Having her first encounter with Dark Samus there, Samus is attacked by the creatures that dwell on Dark Aether, known as "Ing", and has most of her abilities in her Power Suit stolen by them. After further investigation of the Marines' base and reaching the Temple Grounds, Samus defeats an Alpha Splinter and its dark counterpart, recovering something known as an "Energy Transfer Module". Meeting the last surviving sentinel of Aether's alien race, the Luminoth, in U-Mos, Samus is told by U-Mos of the threat the Ing pose to Aether as the Light of Aether serves to maintain balance, and if one version of Aether gets all the light, such as the Ing and Dark Aether, the other Aether will cease to exist. Worse, the Ing may go after the Galactic Federation as well. Refusing to let that happen, Samus agrees to aid U-Mos in recovering the Light of Aether from the Ing.
Traveling to the three major parts of Aether in Agon Wastes, Torvus Bog, and Sanctuary Fortress, Samus recovers her abilities from the Ing, and more, and defeats the dark versions of the creatures from Aether possessed by the Ing guarding the Light of Aether in each area: Amorbis in Agon, Chykka in Torvus, and Quadraxis in Sanctuary. With the Light of Aether restored to their light counterparts on Aether, U-Mos asks Samus to travel to the Sky Temple in Dark Aether to recover the last of the Light of Aether from the leader of the Ing, Emperor Ing. Though Samus defeats Emperor Ing and recovers the last of the Light of Aether, without the Light to maintain it, Dark Aether begins to collapse and cease to exist. Samus quickly heads for the portal back to Aether, but is stopped by Dark Samus, forcing her to fight and defeat it before part of the Phazon it blocked the portal with falls away to give Samus the chance to escape before Dark Aether and the Ing are destroyed for good. Returning to U-Mos, Samus finds that the other Luminoth have awoken from their self-induced hibernation with the restoration of their planet and thank Samus for all her efforts. With Aether's weather restored to normal and her gunship repaired, Samus departs Aether for parts unknown.
However, Dark Samus was not completely destroyed, and reformed to plan revenge on Samus.
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After being awoken from her cryostasis hibernation following a nightmare of Dark Samus being reborn, Samus puts on her Varia Suit and readjusts her gunship to be facing the Galactic Federation planet Norion, where the Federation Seventh Fleet is currently in orbit. She is soon surrounded by several Federation Stiletto-class fighters who contact her and request she transmit her security code so they can deem her friend or foe before letting her any closer to the fleet. Once Samus confirms she's friendly, the fighters welcome her back and grant her clearance to land on the flagship, GFS Olympus, before breaking off to let Samus land unhindered. Once aboard the Olympus, Samus makes her way to the Ready Room to meet with Fleet Admiral Castor Dane and her fellow bounty hunters that were summoned by the Federation as well in Rundas, Ghor, and Gandrayda. Once everyone is together, FADM Dane introduces them to the Aurora Unit installed on the Olympus, Aurora Unit 242, who explains that she and her fellow Aurora Units maintain the primary data network of the Galactic Federation, but the system is currently offline due to safety features after it was discovered that a virus had been introduced into the network, and the Aurora Units shut down to prevent the virus from spreading. FADM Dane reveals that some time ago, the Space Pirates boarded and raided the GFS Valhalla during a training mission to capture its Aurora Unit, 313, and that's how they injected the virus into the system. Dane goes on to further explain that they need the bounty hunters to travel around the area and administer the vaccine to the other Aurora Units and get the system back to full strength, while also investigating what the Space Pirates are up to.
However, the fleet goes to Red Alert when the Space Pirates suddenly emerge from a wormhole right on top of the fleet and send troops to attack Norion's main base that controls the planet's defense systems along with the fleet itself. Dane orders the bounty hunters to not only defend the Olympus but to get planet-side to stop the pirates from sabotaging Norion's defense grid. Samus does her best to protect the flagship and get back to the hangar to get on her gunship and had down to Norion. Once planet-side, the situation is bad: The pirates have disabled the three primary generators that run the defense grid, and as Samus and the other bounty hunters work to get them back online, Dane reports in on something that even he is left at a loss of words on when a massive object appears from a wormhole, heading straight for Norion. Realizing the pirates intend to crash it into the planet, Dane orders Samus and the others to hurry. Despite interference from Meta Ridley, Samus is able to restores the last generator to full power, restoring the defense grid, and not a moment too soon as the object is minutes away from impacting Norion. AU 242 warns her to hurry before it is too late. Hurrying to the elevator to the control tower that runs the planetary defenses, the bounty hunters reach the top, only to be intercepted by Metroid Prime/Dark Samus herself. When it is clear they will be able to stop the object from impacting Norion, Dark Samus blasts them with a concentrated blast of Phazon, which knocks out Rundas, Ghor, and Gandrayda, but Samus, with her last ounces of strength, is able to get the cannon online just in time to destroy the object, saving Norion, before she too passes out.
Fast forward one month later, and Samus awakens back aboard the Olympus in the medical bay, where the female crew member watching over her explains what happened in the meantime since the Battle of Norion: When Dark Samus blasted Samus and the other bounty hunters with her Phazon attack, it caused the bounty hunters to become infected with Phazon themselves, so they were self-generating it within their bloodstreams. To help them adapt, they were each given a Phazon Enhancement Device, or PED, to allow them to use the Phazon within them to power up their attacks. As for what the pirates tried to crash into Norion, it was learned that similar objects had already been imbedded in the nearby planets of Bryyo and Elysia. Rundas headed to Bryyo to investigate that object, while Ghor was sent to Elysia to check out that one. Gandrayda was assigned to seek out the Space Pirate Homeworld. However, contact with the other bounty hunters has been lost for some time, so the fleet, nor the Federation, knows what became of them and fear the worst. After Samus tests out her PED and meets AU 242 in its private chambers on the Olympus, she is assigned to pick up where her fellow bounty hunters left off and investigate Bryyo and Elysia. In the meantime, the fleet is disengaging from Norion and will be out of contact for some time.
As Samus makes her way to Bryyo, during one attempt with using the Hypermode of her PED, she suddenly finds herself unable to exit it normally and is forced to keep discharging Phazon until the suit's automated emergency venting kicks in. AU 242 picks up the anomaly with Samus and promises to look into it, later revealing that the Phazon in Samus can potentially turn corrupted when in Hypermode and if Samus does not discharge it until the emergency auto-vent kicks in, she could turn into another Dark Samus from total corruption. Tragically, this is what befell Samus' fellow bounty hunters.
When Samus finds Rundas, he has already succumbed to his PED Phazon corruption and attacks her, forcing her to fight him. When he is defeated, he appears to regain control of himself, but is then impaled by his own icicle, before an apparition of Dark Samus arrives to collect his remains and leave Rundas' ice missiles behind for Samus to use. Despite that, Samus deals with the anti-aircraft guns that guard the generators for the shield around the Leviathan Seed, and then deactivates or has her gunship destroy the generators in a strafing run, leaving the seed vulnerable. Entering it, Samus fights the guardian of the seed, Mogenar, but upon its destruction, the Phazon in Samus grows and her corruption gets worse, causing her to temporarily remove her helmet as she throws up pure radioactive Phazon sludge because of it. Nevertheless, she then sees to the end of the Leviathan Seed, then moves on to Elysia.
There, she helps get Aurora Unit 217 back up and running, and he explains that to reach the Leviathan Seed on Elysia, Samus will have to take out the shield using, of all things, a thermonuclear weapon. Before she can do that, her gunship requests aid, as it is being attacked by Ghor, who has also succumbed to his PED Phazon corruption. Samus fights Ghor in his battle mech and defeats him, but when the suit explodes afterwards, Ghor is helpless as the apparition of Dark Samus arrives to claim him too. Samus tries to protect him, but the apparition will not be denied feeding on Ghor's remains, leaving his plasma beam behind for Samus to use. Once Samus is able to build the nuke and deliver it to the Leviathan Seed to take out the shield, she then sets about entering it and fighting its guardian, Helios. With Helios' demise, Samus becomes further infected and corrupted, but still manages to take out the seed, thus freeing all the Federation planets from infection by the Leviathans.
After that, Samus' next stop is locating the Pirate Homeworld. When she does, she soon learns that the weather is so bad, she needs a Hazmat Suit that the pirates mass produce to protect her from the acid rain caused by the pirates' heavy industry. While doing so, she rescues a Federation Marine that had apparently not been captured and executed by the pirates, but upon once the Marine helps Samus get closer to acquiring a Hazmat Suit, it turns out that the Marine was really Gandrayda, who like Rundas and Ghor, had succumbed to her PED Phazon corruption, and become one of Dark Samus' top lieutenants in the Space Pirates after her corruption, apparently having better control of it compared to Rundas and Ghor. Thus, Samus is forced to fight the shapeshifting bounty hunter, and despite all the moves Gandrayda uses against Samus, either as herself, or in one of her shapeshifted forms, including a doppelganger of Samus herself in her normal Varia Suit, Gandrayda is overpowered and bested in combat. As her shapeshifting powers go wild on her, causing her to transform into several things, the last thing she turns into, is Samus in her current corrupted appearance, reaching out to Samus and screaming, as if to foreshadow that this will be Samus' fate like the other bounty hunters. Samus can only look away and clench her fist in anger before Dark Samus' apparition arrives to claim what's left of Gandrayda like the other bounty hunters and depart, leaving Gandrayda's Grapple Voltage behind for Samus to use.
Nevertheless, Samus acquires a Hazmat Suit, and disables the planetary shield, allowing FADM Dane and the Seventh Fleet to arrive to lay siege to the planet. Dane himself personally leads a group of Demolition Troopers to help clear the way to the Leviathan Seed for Samus to destroy it. Though she has to face Meta Ridley reborn as Omega Ridley, she defeats him, but her Phazon corruption gets even worse afterwards. Once the seed is destroyed, she then helps to secure another one that has been converted into a battleship for the pirates, using it to create a wormhole for the Seventh Fleet to use to travel to Dark Samus' main base, the planet Phaaze. As soon as Samus lands and leaves her gunship, Phaaze's pure Phazon atmosphere sends her corruption to near critical levels, forcing her to vent all her energy tanks to stay in a permanent Hypermode, but knows that she could become terminally corrupted if she does not hurry and find Dark Samus and finally slay the reborn Metroid Prime once and for all. Upon finding Dark Samus, Samus faces her in battle, and though after being bested, Dark Samus tries to keep the fight going by bringing the Aurora Unit 313 that it captured from the Valhalla into the fight. When that is destroyed, so is Dark Samus, once and for all.
Dark Samus' demise also causes the Phazon corruption in Samus to completely shrink and disappear, leaving her healthy and Phazon-free at long last, but it also causes Phaaze to become unstable and threaten to explode. FADM Dane has the Seventh Fleet retreat to safety back through the wormhole from the Leviathan battleship, but once in the clear, it is apparent that the fleet did not escape from Phaaze without heavy losses: 37% of the fleet has been destroyed, and the rest report heavy casualties. When Dane inquired about Samus, it appears she sacrificed herself to end Dark Samus' threat once and for all, but then Samus' gunship appears, showing she's alright, and transmits to Dane the message "Mission Accomplished".
Returning to Elysia, Samus mourns the loss of her fellow bounty hunters, before taking off for another mission, unaware that she's being followed by Sylux; a mysterious bounty hunter who acts against the Galactic Federation and it's allies.
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Following the destruction of Phaaze, the Space Pirates no longer have access to Phazon as it was utterly obliterated, but it wasn't the end of their threats, when the Galactic Federation found that the Space Pirates were present in the Bermuda System, Samus was once again hired to help discover what was going on there. The Bermuda System is a three-planet solar system and is found to have several abandoned Galactic Federation facilities. It was there where she meets the Federation Force, a team of four elite soldiers with Mech Suits modeled after her own Power Suit and works alongside them up to saving them from the Rohkor Beetle. She mostly assists with gathering much intelligence for them.
Eventually, Samus is taken captive by the Space Pirates and imprisoned on their Doomseye Mothership. She was then brainwashed into doing their bidding. When the Federation Force made their arrival, they increased Samus's size where she is forced to fight them, against her will. The Federation Force managed to defeat her, and she was seemingly buried under falling debris. The impact had managed to snap her out of the trance, and after coming around, she managed to save the Federation Force from the Elite Pirates and she managed to come to the rescue when the Force when they were pulled into space. She tells them that it was an honor to fight alongside them and was grateful to them for saving both her and the universe.
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Samus Aran is set to return in the 2025 sequel to Metroid Prime 3 Corruption. 
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What occurred after that isn't known, but what is known is that the Galactic Federation has made the decision that the Metroids are too dangerous to be kept alive any longer, especially since they kept falling into the hands of the Space Pirates, so they need to be exterminated once and for all. After they failed to do so twice, they once again hired Samus Aran to deal with the recurring threats, which they discovered on the planet SR388, given that she dealt with the Metroids the most.
When she arrived on SR388, Samus observed how the planet's different environments caused the Metroids to metamorphosise into several different forms, each of them much more powerful than the last. She also discovered the ancient ruins of the Chozo that once lived there, which had a golden seal that was connected to the purple-colored liquid which restricted access to the deeper areas of the planet and each time she destroyed all the Metroids in one area, the seal would drop the liquid levels to allow her access to the lower levels where she finds the stronger Metroids. Eventually upon reaching the deepest part of the planet, Samus encounters the Queen Metroid, who is the one who has been reproducing the entire Metroid species and she managed to destroy the beast and believed that she truly obliterated the Metroids forever. However, as she heads down the tunnels, she finds a single Metroid egg which would hatch leading to the birth of the Baby Metroid. Samus was about to kill it, but she holds her fire when she saw that the baby wasn't attacking her as she was expecting and decides to not only spare its life, but also to take it with her. 
As the two of them make it to the planet's surface, the Baby Metroid is suddenly swiped by Samus's long time enemy, Ridley, whose body has regenerated since Corruption and because of its recovery from its injuries and Phazon Corruption, it has no need for its cybernic parts anymore. Samus and Ridley fight over the Metroid hatchling with Samus getting a hold of Ridley's tail when it tried to fly away and shoots a charged shot at its abdomen at a blank point range where Ridley was forced to release the hatchling before shooting at its wing which sends him off a cliff. But Ridley wasn't done with them as he ambushed Samus and blocked her attacks, tossed her against a wall, and was about to finish her off. Fortunately for Samus, she was saved by the baby when it drains Ridley of much of its energy, in order to rejuvenate her, and she finally stood victorious over her arch-nemesis. After that, Samus and the Baby Metroid board the Gunship and leave the planet together.
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Since her adventure on SR388, Samus saw how much value the Baby Metroid would be for the Galactic Federation, so she goes to the Ceres Space Colony and delivers it to the scientists there, so they can study it in hopes of using its power for the greater good of mankind. They have made some amazing discoveries of its potential and Samus left the Station, and it wasn't too long before she received a distress call from Ceres Space Station and turns around to find out that it was being attacked by the Space Pirates and the scientists there are killed, for the purpose of stealing the baby. Ridley itself managed to capture the baby and despite Samus's best efforts to take it back, it escaped leaving the station to self-destruct. Samus managed to escape in her Gunship just before it exploded and pursues Ridley and the baby to Zebes.
Samus found that the Space Pirates have rebuilt their old base of operations and they plan to clone the Metroids through using the baby as its subject. Mother Brain went back to being the boss running this base alongside Kraid and Ridley, with two new Pirate generals being added to their ranks: Draygon, a huge Ervir who resides in Maridia and Phantoon, a surreal being that haunts the Wrecked Ship. When Samus managed to defeat all of them, she heads to Tourian which became accessible, and starts to destroy the Metroids cloned by the Space Pirates discovered there, and she is suddenly ambushed by a gigantic Metroid, which is the largest one she ever saw. None of her weapons were working against it and she was drained to critical levels before it suddenly releases her upon realizing that it was attacking its 'mother' and stops itself before fleeing from the area in remorse.
Samus delved deeper through Tourian until she runs into Mother Brain and destroyed the tank as she had done previously. Mother Brain was supposedly defeated before it suddenly emerged from the debris in a massive hideous form. Samus fought her as hard as ever but Mother Brain used her Laser Brain attack, leaving Samus close to the end of her life. Before Mother Brain could finish her off, the Baby Metroid suddenly appeared and drained the beast of her energy and transfers that energy into Samus to renew her strength. Mother Brain was still alive and she used an energy shot to slay the Baby Metroid. Samus, now at full power, used the monster’s Hyper Beam against Mother Brain and successfully killed her. This caused a self-destruct sequence, which is extended to the planet itself. Samus managed to make it off the planet of Zebes, the planet where she grew up on and the ancient home of the Chozo, was permanently destroyed.
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Samus awakens in the quarantine room where she had a dream of her battle with Mother Brain and the recent loss of the baby Metroid. After going through a training session, she was free to leave and as she flies in her Gunship, she receives a distress call dubbed the “Baby’s Cry” which reminds her of the baby that traveled with her. She arrives at the BOTTLE SHIP which she discovers to be the property of the Galactic Federation and she soon runs into a small group of soldiers and they almost clash until a certain man recognized her and asks if she remembers him, addressing her as “Princess” and removing his visor. Samus then recognized him as Anthony Higgs, and she also noticed that Adam Malkovich is also here as well and he forbids his troops from sharing any information with her regarding the Galactic Federation’s motives, referring to her as an “outsider”. She opens the Red Blast Shield with her missile, to the chagrin of most members except Anthony, who was amused. They find a dead scientist in the next room and Lyle panics at the sight of a Brug and kicks it away while unloading ammo upon it. Soon an army of Brugs appears and form into a Brug Mass which is dispatched by Samus and the Platoon. Adam then permits her to join them on the condition that she takes orders from him.
Samus’s directives bring her to three sectors, which each having a different environment stimulation. Samus comes across adversaries that she is familiar with as well as those she never encountered before, which included Nightmare and RB176 Ferrocrusher, piloted by an assassin that Samus dubs the Deleter. She comes across a blonde woman who claims that she is Madeline Bergman, and she tells her that a rogue group of Federation agents have been modifying life-forms to use as bioweapons, which is clearly against Federation protocol. To counter anyone who tries to investigate what they are doing, this group hired an assassin to silence anyone who learns the truth behind their motives, and this assassin managed to join the 07th Platoon, and he was successful in killing Maurice and K.G. and attempted to do the same thing to her and Adam. Samus is shocked when she learns that Mother Brain’s A.I. was used to create an android for the purpose of controlling the Metroids, which have long been believed to have been eliminated. This DNA from her Power Suit also led to the unintentional cloning of Ridley.
Samus resolves to find the rogue agent and to put an end to the ongoing situation, and she comes across the real Madeline Bergman and it was revealed that she and the other scientists have created the Queen Metroid by accident and while it has been a tough battle, which isn’t helped by the recent death of Adam, the emergency brakes in the ship have been applied which gave her an advantage and defeats the Queen. She learns that the blonde woman she met earlier is an android named MB, whom Madeline also called Melissa to help make her feel more human. They would soon defeat the android in a heated confrontation, and Samus eventually leaves the BOTTLE SHIP with Anthony and Madeline in tow. When she learns that the BOTTLE SHIP is set to be destroyed, Samus rushes back to the BOTTLE SHIP to retrieve Adam’s helmet which she calls an irreplaceable item and she finds herself battling against Phantoon, which she then defeats. It was then that the self-destruct sequence is initiated, and she runs back to her Gunship while in her Zero Suit and puts the helmet in the seat beside her and thinks back to her experience on the ship as she makes her escape from the BOTTLE SHIP’s impending destruction.
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Returning to SR388 with researchers from Biologic Space Laboratories, Samus and two of the researchers enter a cave to find a lone Hornoad there. Having the researchers stay back, Samus shoots and kills the Hornoad with her missiles, but the Hornoad transforms into some sort of gelatinous creature that then attacks Samus. When there were initially no ill effects from it, Samus escorts the B.S.L. ship to their next destination, but during the trip, Samus blacks out at the controls and her gunship drifts into an asteroid belt and crashes. Luckily, the automated systems jettisoned her to safety in an escape pod before impact, and the B.S.L. ship recovered her and transported her immediately back to the Galactic Federation HQ for urgent medical treatment. The creature that attacked her was identified as a parasite known as "X". It infects a host's central nervous system and asexually reproduces, killing the host while stealing their DNA and genetic makeup to essentially create a clone of the victim, even one more powerful and mutated from the original host. When it was clear Samus had a very low chance of survival from the infection as some of her Power Suit was already integrated into her central nervous system, it was decided to try and inject Samus with a vaccine cultivated from the Baby Metroid she had rescued previously. Once injected into Samus' body, the X died off almost instantaneously, saving her life, and revealing that the Metroids were the natural predators of the X, so when Samus exterminated the Metroids on SR388, she unknowingly gave the X the opportunity to recover and increase their numbers. Soon, word comes that an explosion has occurred on the B.S.L. research station in orbit over SR388, where the X and pieces of Samus' infected Power Suit were sent for further analysis. Samus heads there immediately to investigate and find out what went wrong.
Arriving on the station and making her way to the Quarantine Bay, Samus finds that something blasted their way out of their containment unit and freed the rest of the X as well. After fighting an Arachnus made from several X and a Core-X carrying her Morph Ball ability, Samus is told to head to the first of the individual sectors on the station where X have infiltrated the biomes in Sector 1 (SRX), a replica of the environment on SR388. Just after she descends the main elevator to the sectors, a figure that looks like Samus in her Power Suit blasts through the wall, but upon closer look, has no irises or pupils in their eyes. Just an empty, soulless look, before blasting the hatch apart with a Super Missile and continuing onward. By the time Samus reaches Sector 2 (TRO), her gunship's AI, which she named after her former CO, Adam Malkovich, reveals that the figure seen earlier is an X-mimic of Samus, which is dubbed the "Samus Aran-X", or "SA-X". Since the SA-X is armed with all of Samus' powers and abilities, including the Ice Beam, Samus stands no chance against it due to the Metroid DNA now in her blood rendering her vulnerable to the Ice Beam, along with extreme heat and cold temperatures. She's forced to hide from the SA-X whenever in the same room until it is gone to avoid being killed by it as she works to fight the X infesting the station and recover her abilities from all the creatures the X are imitating or from Data Rooms that the Federation are sending upgrades to her through. However, at one point, an X mimicking one of the scientists on the station sabotages the cooling unit for the main boiler in Sector 3 (PYR), threatening to set off the station's auto-destruct explosives if the boiler goes critical. Samus stops it, but it raises suspicion that the X see Samus as a major threat and tried to eliminate her at the cost of their own lives in the process. After further exploration through Sector 4 (AQA), Sector 5 (ARC), and Sector 6 (NOC), Samus is told to head back to the Main Deck due to non-X life signs being detected on the Habitation Deck. When Samus gets there, she finds the life signs to be some old friends, the Etecoons and the Dachora, whom she frees from the room they were in, and they head to the Docking Bays to find refuge on Samus' gunship.
Soon, power goes out throughout the station, and it is due to plant growth choking the main reactor. Samus makes her way to the Auxiliary Power Station to activate the backup power, then makes her way through Sector 2 to locate the source of the plant growth and destroy it. As things continue, she soon locates a strange passageway that is blocked by a shutter that can only be opened from the other side in Sector 6, triggering an alarm that summons the Security Robot B.O.X. she had fought earlier in Sector 3 to investigate, forcing Samus to fight it again and then deal with its organic brain that had been possessed by the X. After beating it, she uses her Wave Beam to investigate the shutter and discovers the Restricted Laboratory where the Federation was secretly breeding Metroids. Unfortunately, the SA-X followed Samus and began laying waste to the lab, freeing the infant Metroids, who immediately go after their prey in the SA-X, overwhelming it. However, the fires that the SA-X caused trigger the lab's emergency isolation lockdown, and Samus barely escapes before the lab is jettisoned and destroyed, killing the Metroids and SA-X.
However, Samus learns that the SA-X reproduced and there are at least another 10 lurking around the station, hunting her down. Worse, the Federation is on their way to capture the X and SA-X to potentially use them for warfare. Knowing if they infect the Federation crews the X will spread like wildfire across the galaxy, Samus intends to stop them. Her AI refuses to let that happen and locks her in the Navigation Room, but when she calls it "Adam", Adam's original personality resurfaces and suggests that Samus redirect the station to impact SR388, killing the X on the station and the planet, saving the universe at large. Making her way to the Operations Deck, Samus is engaged by one of the SA-X before she can reach the bridge, and after overpowering it, it transforms itself into a mutant monstrosity of both Samus and the Hornoad that it originally imitated before infecting Samus. Even then, Samus overpowers it, forcing it to revert to its Core-X form, which Samus easily overwhelms, but the X escapes before Samus can absorb it. After Samus sets the collision course, she evacs to the Docking Bays, only to find the airlock doors blasted open, and her gunship nowhere to be found. Worse, a Metroid survived the Restricted Lab's destruction and had evolved into an Omega Metroid, which manages to reduce Samus to within an inch of her life before the SA-X reappears, seeing the Omega Metroid as the bigger threat compared to Samus with her Metroid DNA and engaging it itself to protect Samus, but whatever vitality it recovered after fighting Samus is no match for the Omega Metroid's claws and the SA-X is quickly reverted back to its Core-X state, which Samus then absorbs herself to regain her Ice Beam and defeat the Omega Metroid personally. With the Omega Metroid eliminated, Samus' gunship returns to pick her up and evac before the station enters reentry and impacts SR388, destroying both the station and the planet, and wiping out the X. Afterwards, ADAM reveals that it had a little help piloting the ship from the Etecoons and Dachora to rescue Samus.
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Unfortunately, Samus learns that, despite the destruction of the X on the B.S.L. station and SR388, some had escaped to the planet ZDR and were trying to rebuild their existence. The Federation sent some robots known as E.M.M.I.s to deal with them, but they've lost contact with the robots. Samus is sent to investigate, and soon learns of the survival of two Chozo warriors from two separate tribes: Quiet Robe, from the scientific Thoha tribe, and Raven Beak, from the warrior Mawkin tribe. When the Metroids were bred by the Chozo, Raven Beak wanted to use them as bioweapons against the universe. Quiet Robe was the lone Thoha survivor so he could control the Metroids with his Thoha DNA while Raven Beak slaughtered the rest. Quiet Robe reprogrammed the E.M.M.I.s to lure Samus to ZDR so Raven Beak could use her Metroid-infused DNA to revive the Metroids to carry out his endgame. Although Samus promises Quiet Robe she'll stop Raven Beak's plan, Quiet Robe is assassinated by one of Raven Beak's robot soldiers right before her eyes as he had outlived his usefulness.
Although hesitant to do it, Samus releases the X stored on ZDR back into the wild to infect and take over. When confronted by the lone surviving E.M.M.I. robot, Samus uses her awakening Metroid powers to drain it of its energy and save herself. When she later confronts Raven Beak on his floating fortress of Itorash, Raven Beak overpowers her and begins strangling her to death, taunting her that he only kept her alive until she awakened her Metroid powers. Now he intends to clone her to have a veritable army of Samus to take over the universe, and she will be just another footnote in the history of the Chozo and Metroid kind. However, Raven Beak pushed Samus too far, and in a state of absolute fury, Samus transforms her Power Suit into the Metroid Suit, fully embracing her Metroid powers and DNA in her blood, and easily overpowers a now terrified Raven Beak, draining him of his energy without mercy, and doing the same to Itorash, causing it to crash. When Samus recovers, Raven Beak is infected with an X parasite, transforming him into some sort of abhorrent abomination of himself, Kraid, and other creatures that the X possessed the DNA of. Samus simply blasts him with her Hyper Beam, not only forcing the X back into its gelatinous form, but then blasting that into oblivion, ensuring Raven Beak's death once and for all. Hurrying back to her gunship, she arrives with moments to spare before ZDR explodes, but before she can activate her gunship, ADAM stops her, warning her that her Metroid Suit will drain the ship's energy, leaving them unable to fly off the doomed planet. Luckily, an X-Parasite mimicking Quiet Robe appears, and acting on the Chozo's benevolent nature, it willingly lets itself be absorbed by Samus to restore her Power Suit to normal, thereby suppressing her Metroid powers. With the issue resolved, Samus quickly fires up her gunship and escapes ZDR just as the planet is blown to smithereens.
Category:Synopsis