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This chapter picks up where Volume 1 left off, with Ridley mocking Samus for being the bioweapon that Mother Brain was talking about. Ridley goes on to tell her that to survive the explosion on the Afloraltite, he had to eat the flesh of the dead humans, and also taunts her as to say that Virginia Aran, her mother, may have been one of his meals. All this causes Samus to fall into a state of posttraumatic stress disorder and falls to the ground in silence, her Power Suit disappearing. Grey Voice commands Ridley to stop, to which he replies that he will not take orders from Grey Voice until he "gets his hands dirty" and kills Samus himself.
Meanwhile Mauk, Kreatz and Pyonchi discover Chozo labs being used on Pirates to "adjust their bodies so they can adapt to this planet." In the same lab they find twelve to thirteen Chozo prisoners, including Platinum Chest, the Chozo who helped Mauk's race join the Federation. Mauk and Kreatz make plans to over throw the guards but just before they attack Ridley, Grey Voice and Samus walk in. Grey Voice refuses to kill Samus, saying that the Chozo have a mental guard making them "incapable of harmful actions" and that Samus may still defect to the Space Pirates. Ridley then turns to the prisoners and, with Grey Voice's approval, moves to attack them.
9: Counter AttackEdit
Ridley advances on Platinum Chest, and proceeds to strangle him with his tail. Seeing this, Mauk remotely activates the ship they arrived in and fires on the "heat sources" on the planet, in hope of causing a distraction and saving Platinum Chest's life. The plan works, and Ridley releases Platinum Chest and turns back to Samus, demanding to know where her back up is coming from. Grey Voice dismisses this idea, saying Samus was trained to work alone. He goes on to say that she alone knows this enviroment, so the explosions may have been "planned ahead of time" to allow her to escape. Grey Voice then orders the Space Pirates to find the ship while Ridley orders the prisoners to fix the Body Adaptation Machines, destroyed in the explosions. Satisfied that Grey Voice is acting as a Space Pirate Commander, Ridley flies away to help in the search. Grey Voice dismisses Samus as pitiful and leaves her alone.
Mauk and Kreatz then come out of hiding to free the prisoners, but as they turn to Samus, they find her begging for them to kill her.
10: Phoenix IEdit
Samus screams "He hunted them like animals, it's hopeless to run, so kill me before it happens." Platinum Chest deduces that Samus has supressed memories of the attack of K-2L long ago, and is in shock. The Chozo surround and place hands on her, telling her to let out her sadness and anger. Meanwhile, Ridley receives the full status report on the broken equipment hit by the ship's missiles, when the news comes through from Grey Voice that the prisoners have escaped. Flying down to the port, Ridley finds Mauk and Kreatz fighting off the Space Pirates. He attempts to attack the Chozo from behind, but as he is about to strike, Samus re-dons her Power Suit and blasts Ridley in the chest, sending him flying away, stating that "Protecting the protectors is [her] duty".
11: Phoenix IIEdit
Samus's worries change to Mauk and Kreatz who will not manage to cope with the oncoming Acid Rain, and starts planning a detour though Brinstar while assuring Kreatz that she is alright. As the team moves on to Brinstar, Grey Voice watches them and reflects on Samus' maturity. Samus notices that her suit has resonated, and Platinum Chest claims that Grey Voice left.
Meanwhile, in Mother Brain's chamber, Grey Voice breaks in dressed in 100 year old Chozo battle armor and with a staff weapon, he destroys the entrance, announcing "he has come to settle things". He attacks Mother Brain's Control Capsule with the staff weapon, until he falls to his knees. Mother Brain states that his attack will be a risk to his life due to the pain he is suffering overcoming the Chozo mental guard. Grey Voice gets up and announces that he "must redeem our senseless deeds" and that the "defective product" of Mother Brain "must be destroyed".
Mother Brain replies that she thought that Grey Voice was "the only one who was wise" but he turned out foolish. Grey Voice, still attacking Mother Brain, tells her that "You will not be building the new Era, you are not the Successor ... You are afraid of life and the potential of the races... You're jealous of life and the future". Mother Brain denies any of this, saying "She was born to the True Master of the Universe".
Grey Voice makes one last accusation, that Mother Brain is jealous of Samus.
12: Phoenix IIIEdit
Re-emerging from the caves of Brinstar, the team find a Chozo ship. Platinum Chest is still discussing Grey Voice with Samus, the fact that it was always intended that he would turn against Mother Brain, though the timing of Samus's arrival complicated things. Samus feels saddened by this, saying that she can feel his struggle though her Power Suit, and she can hear him shouting "Samus, you must move on." Platinum Chest reveals that Grey Voice was the donor of Samus' Chozo DNA, causing him to be a surrogate father of sorts. Samus nearly abandons her mission to assist in the fight against Mother Brain, but when the Space Pirate Flagship looms over Zebes, they proceed to escape while fighting off several Pirate fighters.
Meanwhile, in Mother Brain's chambers, Grey Voice continues his assault against Mother Brain, saying that Samus constantly changes things to make the future unpredictable. At this time, Ridley bursts in and impales Grey Voice with his tail, though he manages to stumble out of the chamber and into the open, next to a Chozo Statue. Ridley asks if he would like a Chozo grave, while the Chozo destroys the fighters chasing Samus before collapsing on the ground. He uses his mental link to Samus to send her his last message before being blasted by Ridley's plasma breath.
"Samus, I leave the rest to you. You have become strong, so strong. Samus I know that your fate is harsh, but, though this will be hard for you, there are many people in the universe who need your strength, I want you to save them, be it only one or many, I want you to help them, this is my request. You have become strong, my child."
The Chozo ship breaks the atmosphere and notices the Mother Ship looming before them. Just as it looks hopeless, General Adam Malkovich arives in the Federation Army Special Ops Battleship VIXIV, destroying the Mother Ship and stopping the Pirate presence on Zebes. Platinum Chest considers re-grouping with the Chozo survivors while Samus decides to fight in the memory of Grey Voice.
The story picks up a few years later, with the Space Pirates, having rebuilt their base and begun their reliation, now under the leadership of Mother Brain. Mauk, now a commander, replies to a distress signal but is too late, and has found all the people dead, with their energy drained. Mauk instantly recognizes the smell from his trip to Zebes.
On Daiban, Adam Malkovich discusses with Chairman Keaton about the new Pirate strength. Keaton thinks that Mother Brain is sending them a message and that the Federation must "reply to her threats". The scene then shifts to a Samus, clad in a hat and long coat, on a stroll through the streets of Daiban. She passes by Damara and two of her other friends from Jigrad, and stops to congratulate her on her acceptance into the Galactic Federation Academy, leaving Damara bewildered as to how she knows her personally.
At Keaton's inauguration as a chairman, Damara presents Keaton with some flowers to thank him for admitting her into the Acadamy, this alarms Pyonchi, which causes Samus to attempt to run up onto the stage. Stopped by the security guards, she shouts to Adam to throw the flowers, and to everyone's surprise, the flowers metamorphose into a Mimic, a banned Space Pirate bioweapon that was sent to assassinate Keaton. Samus calms a very startled Damara, activates her Power Suit, demands from Adam a payment of 3500 seguru and destroys the monster.
The chapter ends with Damara recognizing Samus from her childhood as Samus is narrating about how she was now "living by her arm, constantly looking for danger and new targets. What the people call a Bounty Hunter."
Mauk, in command of a Federation ship, hears from a crew member that they have found Ridley's army. He then says that they can begin a counter attack. Meanwhile, the Pirate fleet reports that they have found a ship in an asteroid belt, and asks Ridley if they should blast it, although Ridley turns down the suggestion, as he desires revenge on Adam Malkovich. and says they can begin a counter attack.
At Galactic Federation Headquarters, an older Chief Hardy as evidenced by his apparent alopecia totalis, briefs Samus at the request of Adam on the events of SR388. Samus is quick to recognize that the Metroids are the unknown species that was responsible for killing an entire exploration squad, and informs them that the Chozo created them to protect the galaxy from an unspecified threat.
At the Academy, a child is seen bullying a friend of Damara's whom he derogatorily nicknames "Potato Farmer", when Damara demands that he stop defiling the "holy academy" with violence, although the bully continues to harrass "Potato Farmer" until he is mauled by Pyonchi.
Damara, realizing that Pyonchi was the Rabbilis present at Keaton's near-assassination, spots Samus, Adam and Keaton walking off to a military research lab. There, Adam uploads Bomb and Missile Launcher data to Samus' Power Suit whilst chuckling about how Samus is not very feminist. She assures him that she can complete her upcoming Zero Mission successfully, as she has a score to settle with Mother Brain, this type of mission is suited for a Bounty Hunter, and she knows Zebes because she grew up there.
Samus watches a very cheerful Damara playing with Pyonchi and her friends, and with a smile, runs off to complete her mission.
15: Tooth and NailEdit
At the Academy, a teacher informs the students that the Space Pirate Sympathizers have begun terrorizing the galaxy, and the Federation Police Force has yet to regain public order, causing "Potato Farmer" to bemoan about how he will be used as an engineer for war purposes, and argues with his earlier bully.
On Zebes, Mother Brain cackles at the reports of destruction on yet another planet, stating that she will soon become the ruler of the universe. However, she quickly realizes that Samus has landed on Zebes alone and is quickly destroying everything in the ecosystem.
Samus finds that everything on Zebes is trying to kill her, to protect Mother Brain, and she is tripped by the mature Imago and King Worm. After killing them, she asks Mother if these creatures are the two partners she spoke of, and if she desires to rule over a universe of mindless beasts. Mother, in response, states that she expected Samus to be tenacious, and summons Kraid. Samus is quick to find that her weapons are useless on him, and is told that his skin is on par with an anti-optical shield.
She is then pinned down by Kraid's belly spikes while Mother tells her that she is only repeating history. Samus speaks of her determination to fight for the universe and demands that Mother stop playing around, after killing Kraid by exploiting a weakness of tissue in the mouth.
Samus then says to herself that Adam's data came in handy, but she quickly finds herself unable to walk on further. In a mixture of emotions, Samus collapses to the ground, with a spirit approaching her.
16: The SuccessorsEdit
Samus finds the spirit of Grey Voice communicating with her, asking why she is so hurt saying he alone was a sufficient sacrifice in the initial invasion of Zebes. Samus, removing her Power Suit, questions whether what she is doing is right.
Outside Zebes, several battles with Space Pirates are held. In Zebes orbit, the Federation Army Special Ops Battleship VIXIV finds that Ridley's mothership is approaching Zebes. While the fleet thinks they are retreating, Adam believes something happened to Samus on Zebes, and says that she is not only to defeat the enemy, but to return alive. On Jamoru, Mauk battles an army of "damn crabs" for his homeworld when Kreatz appears and assists, while suggesting they help Samus as well.
On Daiban, Keaton asks Damara to get to class, as she sits on ledge worried sick about Samus. Keaton assures her that she will have the chance to welcome her back after she returns.
Back on Zebes, Samus and Grey Voice walk down a hallway, with her chatting about her bounty hunting life. The two soon come across a Chozo Statue, and before Grey disappears, he gives Samus the Varia Suit, a more advanced Power Suit than ever before. A dragon-shaped shadow suddenly appears over Samus; Ridley has arrived. A taunted Samus feels neither fear nor anguish. Seemingly triumphing over her posttraumatic stress disorder, she uses the Wave Beam, Ice Beam and Missiles to finish Ridley off. Samus then searches for Tourian, and the manga closes with her preparing to accomplish her two main objectives of destroying both the Metroids and Mother Brain.