Fragments of a space structure, pulverized by meteors; a small embryo, growing into a child with short blond hair.... a high-pitched shriek finally awakens Samus Aran from her trance. She is on Zebes, battling a monstrous bipedal Mother Brain. She was just moments away from death. "Why am I still alive?" she wonders. It appears that the Metroid infant has come to her rescue, healing and protecting her from the furious attacks of Mother Brain. The infant endures hit after hit, refusing to let go of Samus before she is completely healed. Finally, it releases Samus, ready to attack, but it receives one pounding too much; its energy fragments shower Samus as it explodes, emitting a final cry. This has an unexpected benefit, as the infant's remains now provide Samus with the Hyperbeam. "Mother... time to go!", says Samus in a grimm tone, pointing the Hyperbeam at Mother Brain.
Flash-forward. Samus wakes up at the Galactic Federation Headquarters, where she recuperates from her ordeal. Federation scientists help repair the damage done to her Power Suit, while her final battle with Mother Brain, the destruction of Zebes and the loss of the Metroid infant keep playing in her dreams over and over. One of the scientists mentions they gave her suit a polish, so that it looks like new; time for some taret practice. After her training yields satisfying results, Samus is deemed fit for duty again. She reports back to the Galactic Federation congress with good news: both the Metroids and the Space Pirates have been annihilated. The members of congress are ecstatic; the Galaxy is finally at peace.
Some time later. Samus has slowly taken up her old job, travelling for several months through the Galaxy with her trusted ship, looking for bounty, when she finally receives an SOS message, identified as a Baby's Cry: the most urgent call for help used by the Federation. Following the signal leads her to a large space ship that is vaguely shaped like a bottle. After landing in the ship's docking bay, Samus immediately notices a large Galactic Federation Army ship having already docked there. The sound of distant explosions rock the ship; she follows them, and encounters a group of Galactic Federation marines. One of them is her old friend Anthony Higgs from her days in the army. His squad, platoon 7, is led by her old commander, the tough general Adam Malkovich. A flashback to her days in the Galactic Federation Army show Samus serving in several missions under Malkovich's command. However, a certain unspecified event made her quit the army and started her bounty hunter career. The present-day Adam acts very coldly towards Samus, referring to her as an "outsider". However, after they encounter the dead body of a scientist, and Samus helps them defeat a strange creature consisting of tens of smaller insects, Adam understands that Samus' assistance will be invaluable. She is allowed to help, but under the condition that she obey his every command.
This brings back more memories to her previous career. Samus was naive, inexperienced, the youngest recruit and only female of her squad. She generally disliked taking orders, but she obeyed Adam, and came to see him as a friend, and even father figure. She trusted Adam's judgement and decisions, and as a sign of mutual respect, Adam would often ask Samus "Any objections, Lady?"; where other soldiers would invariably reply with a thumbs-up, Samus would typically taunt Adam by giving him a thumbs-down; partially because the word lady sounded derisive, yet Adam always managed to use it in a respectful manner, acknowledging her difficult past. Despite their falling out, Adam is still the one who understands Samus best.
Adam briefs the men and Samus on their current mission: to gather information on what transpired on the Bottle Ship, but more importantly, search for survivors. Due to the ship's interference, the soldiers will not be able to use their com systems, but Samus' superior system is not negatively affected. After all soldiers are given a designated mission, Samus is ordered to get the electrical system back on-line, with Adam monitoring her progression through the camera in her Power Suit. For the moment, he allows only basic weaponry, in order not to damage the ship parts, but he will authorize use of additional weapons as needed.
While restoring main power, Samus finds out the ship houses many different areas, filled with hostile creatures from many planets, Zebes among them. In sector 1, a lush forest area, Samus hears a strange screech, that seems to attract particularly large and ferocious animals. After defeating them, she comes to a lab called the Breeding Room. It is a holding cell dressed as a habitat to raise some creature. Samus finds another body of a dead scientist. This one shows strange bite marks from an unknown creature, but much smaller than the ones she previously encountered. It gives her a strange chill, like feeling the presence of a dark intelligence. Back in the hall where she heard the screech, Samus discovers a small, white, furry critter, looking somewhat like a cross between a rodent and a bird. It clumsily plays with a large piece of fruit. When noticing Samus, it runs away at first, but then returns, giving her a long and unsettling look. Samus thinks nothing of it and proceeds. She finds out that the illusion of the forest is partially mimicked by holographic walls that can be deactivated by nearby terminals. Proceeding further, she arrives at a canyon-like hall, with a large sleeping creature. Again, there is a distant screech, which awakes the creature and sends it into a frenzy. Samus neutralizes it and moves through a series of service tunnels, that lead her to some subterranean parts of the sector. She arrives in a hall called the Biological experiment room, which houses a large underground beehive. Another high-pitched screech alerts several large bees that start attacking her. She fights them off and destroys their queen, but she is disgusted to notice the furry white critter again, ferociously feasting on the remains of the hive, snarling loudly at her. Could this strange creature be responsible for the screeching and alerting the other creatures? On Adam's orders, Samus advances to the Biosphere test area in the sector.
This so-called Exam Center is a multi-story building standing in a simulated, savannah-like environment. She finds Pvt. James already inside the control room. The other marines also arrive and they notice that Pvt. Lyle is missing. Data from the computer seems to have been erased, but Pvt. Maurice knows how to restore parts of it. During first inspection, Samus finds a room with a deceased, cybernetically enhanced Zebesian Space Pirate, wearing the Galactic Federation insignia. From reconstructed computer data, it appears that the Bottleship is a Federation facility, where diverse life forms have been brought for illegal research to use them as potential bioweapons. The site director is a scientist called Madeline Bergman. While searching the building with the marines for Madeline, Samus gets herself trapped with a group of cybernetic Zebesians. After defeating them, she runs back outside to help the marines fight off a large lizard-like monster. As it notices Samus, it immediately attacks her, but Anthony's plasma rifle wounds the creature just enough to repel it. Pvt. Lyle's deceased body is found in the field, apparently crushed to death. Another startling discovery is made when Samus finds the skin of the rodent-like creature, from which the lizard seemingly hatched. She follows the lizard through sector 3; nobody notices that the Exam Center suddenly explodes. She finally looses track of the creature in a large volcanic area. Adam sends her to look for survivors in sector 2, the arctic habitat. Deep within the sector, she finds a giant ice beast lying dead and almost dried out, as if attacked by Metroids. But as the Metroids have died out and cannot stand cold temperatures, this seems impossible. After traversing long snow-covered caves and large machine rooms, Samus finds herself on a surface area with a building standing nearby. The frozen body of Pvt. Maurice lies in front of it. Samus sees a young blond woman looking at her from inside the building, running away upon being noticed. Samus enters the building and follows the woman, who flees in terror into a storehouse. Despite Samus' reassurances that she is there to rescue her, the woman believes the Galactic Federation has send out a team to kill all survivors; she had witnessed Pvt. Maurice getting killed by another unidentifyable marine some time earlier. Samus manages to calm her down, but then they are suddenly attacked by a large load-lifter, operated by a marine who keeps consciously out of sight, hurling crates at them. Samus saves the woman's life and destroys the machine, but the marine escapes before he can be identified; there is no more sign of the woman either. At that moment, Adam calls in to send Samus to section 3, where the lizard is stirring up more creatures into a frenzy.
Samus contemplates that one of the marines is an assassin, sent by people inside the Federation to silence everyone who knew or learnt about the illegal experiments done inside the Bottle Ship. She decides to call this traitor the Deleter. Unseen by the others, the Deleter shoots and kills another marine and tosses his body into a pool of lava.
Samus makes her way to the volcanic area of sector 2, where she finds Anthony engaged in a fierce battle with a strange insect-like flying creature. She saves his life and together they repell the creature. Anthony tells her that the entire unit has orders from Adam to go to sector 3 and open the magma-eruption port, which will restore power in the sector. However, he was the only one who actually showed up until then. Talking about Adam with Anthony, Samus remembers the event that drove them apart. Adam's team had rescued a commercial spacecraft. But at one point, the drive unit of this craft, which was operated by Adam's younger brother Ian, became highly unstable. Samus begged Adam for permission to go in and save Ian, but Adam knew Samus would never be on time and that it would kill her. He was forced to disconnect the exploding unit from the spacecraft, in order to save its 300 crewmembers and prevent Samus from going to her death. Disillusioned by Adam's seemingly cold sacrifice of his brother, Samus left the military.
She goes through the Blast furnace towards the energy core, where the same insect-creature that had attacked Anthony starts to fight with her. She fights it off and the creature falls down the reactor shaft, seemingly dead. While nearing the magma pool, Samus sees a strange thing hanging on a wall: it is the lizard's skin. Just as with the rodent, its back has ripped open, and something must have emerged from inside. The magma room itself is dark, but Anthony has already made it there. He warns Samus when a big flying shadowy creature passes by. Samus opens the magma-eruption port and restores power to the area, but the lava also forces the attacker out of hiding. With a loud bang, he lands on the platform, and it is a shockingly familiar face: Ridley! The winged dragon, Pirate leader and Samus' eternal nemesis, is back from the dead. The small rodent, the lizard; all have been stages in the life cycle of this nefarious creature. Adam witnesses the scene through Samus' helmet camera and urges her to use her Plasma Beam, but he is suddenly attacked by an unknown assailant, losing his comlink in the struggle. Ridley uses Samus' momentary state of shock to grab her, the shock of the entire event causing her suit to malfunction, but Anthony quickly loads his plasma rifle and uses it to shoot Ridley, who lets go of Samus. Unable to fire another shot from the depleted weapon, Anthony further taunts Ridley to keep him away from Samus, but the dragon pushes him over the edge into the lava pool. Furious, Samus comes to her senses, and once again engages Ridley in a fierce fight. With all her might, her hits finally floor the creature. Though severely wounded, Ridley recovers, breakes a hole through the wall and escapes. Mourning the loss of Anthony, Samus leaves the pool and heads for the Main Sector. Noticing that communications with Adam have ceased, she immediately suspects the Deleter's part in this; from his perspective, Adam coordinates the mission and therefore poses the most danger. At the Main Sector, Samus sees a solitary marine suspiciously walking to the elevators. She decides to follow him silently into the Sector 1 jungle. In Adam's absence, she personally reactivates some of her suit's functions to progress further into the sector, until she ends up at a dead end, a computer room. It appears that the blond woman whom Samus rescued earlier is working there; however, this time, Samus manages to convince her that she is a bounty hunter, and not part of the Galactic Federation.
The woman identifies herself as Madeline Bergman. She explains how certain people within the Federation tried to create a special force of bioweapons modelled after the Space Pirates, consisting of Zebesians. However, the presence of the infant Ridley made the creatures ferocious and uncontrollable. Fearing that the Zebesians would evolve to become Space Pirates again, Madeline sent a distress signal, even though that would endanger her own life. Listening to the story, Samus starts to have her doubts; being a feral species, the Zebesians could never become as highly organised as the Space Pirates without a controlling force such as Mother Brain. Also, why would the Federation agents go through such lengths of sending the Deleter to kill everyone aboard, when they could just as easily destroy the Bottle Ship from space with high-caliber weaponry? Madeline reveals that the Federation had an even more dangerous plan: using cell residue from the killed Metroid baby that had fallen onto Samus Power Suit, the researchers had succeeded in resurrecting Metroids aboard the station (Samus suddenly remembers the Federation technician mentioning that he had "given her suit a polish"). However, Ridley's cell remnants had also attached themselves to Samus' suit after the fight on Zebes, so he was accidentally cloned during this procedure as well. As Ridley's initial fuzzy white form had not arisen suspicion, the researchers had kept it inside the Breeding Room, until it lured one of the scientists inside and killed him. Madeline further explains that, in order to control the Metroids by telepathy, an artificial intelligence called MB was created that reproduced Mother Brain's thought processes. MB and the Metroids were kept in a secret area modelled after Tourian, called Sector Zero. However, as MB communicated with the Metroids, it evolved and became self-aware, just as the real Mother Brain once had; it ran out of control and posed a real danger for the Galaxy again. The Federation agents secretly sent the Deleter with Adam's team to retrieve some Metroid specimens, but kill everything else and destroy the station. Samus' unanticipated presence, however, has disrupted these plans. Samus decides to search for Sector Zero and destroy the threat of MB and the Metroids. Before Samus leaves, however, Madeline identifies Adam Malkovich as the leader of the illegal operations aboard the Bottle Ship. While leaving and pondering this information, Samus does not notice that her entire conversation with Madeline has been watched from a platform above. A marine walks slowly downstairs, closes in on Madeline, and as she turns around, a gunshot is heard.
Samus returns towards the Main Sector, where she again encounters the insect creature, but with her suit upgraded to full power, she finally finishes it. She goes along to Sector 2, to the secret entrance to Sector Zero. This area features some very strange and violent effects, such as reversal of gravity and hypergravity. She makes it to the core, where she finds the source of these effects: a biomechanical creature called the Nightmare, which has the ability to manipulate normal gravity. She keeps hitting it with missiles and beam weapons until it falls down and remains motionless. Samus proceeds, but suddenly, she feels the ships engines being activated; the ship is being launched. She wastes no time and runs to Sector Zero through a long, curved hallway where the lights are activated as soon as she crosses it, until she comes to a very large room with a door on the end. She proceeds cautiously, but she notices that something is watching her. It is a baby Metroid, same as the one she found on SR-388. As it shrieks playfully, Samus hesitates, but she finally brings herself point her weapon at it. But before she gets the chance to fire, she is hit herself, with a weapon that stuns her and deactivates her suit. Lying helplessly on the floor, the small Metroid instinctively sees her as prey, but before it can attack, it is killed by an ice beam.
Samus regains consciousness to find Adam sitting next to her. He explains that he shot her, because the Metroids in Sector Zero most likely cannot be frozen. Since producing bioweapons with a fatal flaw would be most unwise, the researchers have genetically manipulated the Metroids and rid them of their one mortal weakness, their susceptibility to cold; the infant that was shot was only vulnerable because it was in a larval stage. Samus asks him why he is credited as the creator of the Metroid breeding program. He explains that he had insisted with HQ that a Metroid breeding program was a bad idea; but several members of the Federation had co-opted his report for their own purposes. Adam assumes that MB has put the ship on an intercept course with Galactic Federation HQ to start an attack with Metroids on the Federation. He orders Samus to go and divert the ship off its course, locate a survivor who has been detected in room MW, and kill Ridley; he also warns Samus that Madeline Bergman is no ally. In order to kill the indestructible Metroids, Adam plans to go into Sector Zero and create enough damage so it will detach and self-destruct, taking the Metroids and MB with it. As before, Samus desperately pleads to Adam to give her the chance to go in and let her take care of things, but Adam assures her that his sacrifice will be necessary, as Samus is needed to defeat Ridley. Still weakened, Samus is unable to stop Adam from entering Sector Zero. She cries and begs him to stop, but he turns around one final time, saying his signature line "No objections, right Lady?" As always, Samus gives him a thumbs-down. He silently proceeds as the doors close behind him.
The sector dissociates from the Bottle Ship as Adam predicted, and the sound of an explosion signifies Samus that he has succeeded. Understanding Adam's sacrifice, Samus finally recuperates and starts her new missions. As she armours up and runs back, the curved hallway seals behind her and starts to break off from the ship; she is barely able to activate her suit's gravity function to prevent her from being sucked into space. This also negates the hypergravity effects from Sector Zero. Unfortunately, on her way out, she again encounters the Nightmare that wasn't completely dead, but this time, she completely obliterates it. While making her way through Sector 1 however, a severely wounded Ridley is slowly recuperating in room MW. Then a large door opens, something huge exits, and attacks Ridley. Samus once again finds herself in the computer room where she had her talk with Madeline, when she finds a body on the ground; it is Pvt. James, dead. Samus notices that a previously closed hallway is now free to access. A series of corridors and console rooms lead her to a hallway with a large hole in the ceiling, and blood on the floor; clearly Ridley has infiltrated the sector here. To her astonishment, Ridley sits in the adjacent room, completely dried out with an agonized expression on his face. She proceeds to room MW, where she finds a red-haired woman locked inside one of the holding cells. The woman panicks, yelling to Samus to stay away while activating some controls. At that moment, a large door in room MW opens. Samus goes through the doors; the floor is wet and slimy, and Samus discovers a familiar but disturbing sight: broken Metroid eggs! A loud pounding sound announces another grisly but familiar sight: an enormous Metroid Queen! Impervious to Samus normal beam, she jumps away from the creature's quick snap, and fortunately, the beasts size prevents it from giving chase; however, it is produced six mature Metroids to defend her. She quickly freezes and destroys these Metroids, but the Queen does not take kindly to that, and starts breathing fire. The impact of a barrage of Samus' missiles almost brings the creature down, but it manages to get up again. At that moment, the ship's computer announces that the Bottle Ship will reach Federation Space in 30 seconds. As the creature charges while the computer starts the countdown, Samus prepares for one final missile blast, when the ships emergency brakes are suddenly activated. The enormous change in momentum slams the Queen onto her side, giving Samus the opportunity to target the creatures vulnerable underbelly. As the beast roars, Samus latches onto its beak with her Grapple Beam, and pulls herself all the way into the stomach, where a Power Bomb finally blows the Queen violently apart.
Room MW lies in ruins as the red-haired woman leaves her broken holding cell and escapes, followed by Samus. She tracks her down to a large hall, and manages to calm her down. The woman identifies herself as Madeline Bergman, the one responsible for all operations. Samus doesn't believe it, but the woman positively verifies her identity with her badge. The blond woman who previously identified herself as Madeline, the 'fake' Madeline, turns out to be the artificial life form MB, an android with the intellectual data of Mother Brain. MB was created as a copy of Mother Brain, to regenerate and control the Space Pirate forces telepathically. In time, she was thought to be capable of controlling Metroids as well, so a cloning program was started in sector Zero to create unfreezable Metroids. Before that, one of the normal Metroids unexpectedly matured into a Queen, while normally only infants with special genetic coding would become Queens. The scientists kept the unaltered Queen as a control specimen. Inspired by Samus' relationship with the baby Metroid, they gave MB a human appearance so that the Metroid hatchlings would come to recognize her as their mother. MB in human form quickly humanized and displayed learning abilities beyond expectations. Madeline decided to call her Melissa Bergman, and came to see her as a daughter. However, Melissa also started to develop emotions and became increasingly self-aware and rebellious; perhaps her extensive contact with Metroids humanized her to extreme extents. The scientists decided to remove her consciousness and emotions so she would be better to control. When they restrained her, Madeline knew painfully well that it needed to be done, and it caused a massive reaction in Melissa: in a fit of rage, she killed her captors and telepathically sent the Space Pirates aboard into a frenzy, killing nearly everyone. She wanted to get revenge on humanity by attacking the Galactic Federation, but this plan was thwarted by the appearance of Samus and the marines. All of a sudden, Samus and Madeline notice that MB is standing in the hall with them, holding a gun. She holds Samus responsible for the failure of her plan. Madeline tries to reason with her, but MB quickly attacks her before Samus can stop her. But then, suddenly, an Ice Beam hits Melissa. A platoon of Galactic marines enter the room, holding Samus at gunpoint, not noticing that MB is quickly thawing out. MB throws away her gun and fires a massive telepathic wave, which enrages the remaining creatures on board and awakens some fierce insectoid Desbrachians that were disguised as hemi-spherical ornaments on the walls. In the ensuing chaos, the creatures attack the marines with ferocity, but Samus is just able to lock onto MB with her gun; just before she fires, she is stopped by Madeline, holding MB's gun and firing an Ice Beam at MB. A voice yells "fire!" as the marines discharge their guns on MB, with Madeline screaming in horror. No longer under outside control, the insectoids immediately retract into their hemi-spherical shields, as Madeline sobs wildly at MB's lifeless body. A marine general steps forward to Samus, commending her on a job well done. As marines take Madeline away, the general laments the loss of Cmr. Malkovich and his entire team, which, according to him, voids all of Adam's orders, making Samus an outsider again. Due to that, he denies Samus further contact with the witness and orderes a marine to escort her out. However, while taking her, the marine identifies himself as Anthony Higgs. With Anthony the only remaining team member, Adam's original order of securing survivors onboard the ship, as ordered by the Galactic Federation, and his approval of Samus' assistance, still stands, leaving the general no other choice than to let Samus and Anthony leave with Madeline. Aboard Samus' ship, Anthony reveals that he survived his fall in the lava by quickly freezing it with an Ice Beam, and that he was the one who activated the ship's brakes. Madeline falls asleep, exhausted with emotion. Samus ponders that Madeline would have some explaining to do at the Galactic Federation Headquarters, which could have been destroyed if she and the team had not been there to stop MB. Samus still has some sympathy for MB: her consciousness was regarded as insanity by her human creators, but they simply drove her to violence out of their greed and distorted ideas. Samus thinks about the genetically manipulated Metroids, and what could have happened if Adam had not recognized the danger they posed to civilization. Unfortunately, it cost him his life; his decision to sacrifice himself was a thing that Samus will have to learn to accept.
Back at GF HQ, Samus finally comes to terms with Adam's decision. Silently, she gives him a final thumbs up. Anthony, who is watching her, cheerfully copies her usual thumbs down as they leave in good spirits.
Some time later, as the decision has been made to destroy the Bottle Ship, Samus makes her way for one final job, to collect an irreplaceable object before the ship is obliterated. The ship is still as dangerous as it ever was, especially the Desbrachians give her a hard time. They keep passageways hidden, but with help of the Power Bombs, Samus defeats them and enters formerly restricted areas, such as the residential area, and finally reaches the ships Control Bridge. There, it appears that Ridley is not the only ghost from the past that has returned: Phantoon, the octopus-like ghost from Zebes, suddenly appears outside the window, many times his previous size, and attacks her. Knowing her enemy, Samus gets rid of this final fiend and continues to the command room where Adam had been observing and commanding the mission. Samus' desired object lies silently on the table: Adam's helmet. She deactivates her suit and picks it up. It brings emotional thoughts to Samus, about how Adam must have seen her talking to the fake Madeline, not being able to tell her that it was MB; how he left to warn her, and in his hurry, forgot the helmet. But there is little time to linger on the past: the ship starts a countdown to its imminent destruction. Not wanting to risk any harm to the helmet, Samus decides to leave her Power suit deactivated, and armed with only her stun gun, she escapes while parts of the ship collapse behind her and Space Pirates try to shoot her. She reaches her ship and takes off. "Sorry for keeping you waiting, Adam", she says, as the Bottle Ship explodes and her ship flies away: "Time to go home."