On an Earth right next to this one, Khan returns to his ship through a dimensional transit portal. Immediately, one of his soldiers calls out "All Hail Khan". Not interested in ceremony, Khan tells them to "never mind that". Instead of receiving honor, Khan chooses to show it to his foe Storm, one of the X-Men, whom Khan now carries in his arms. Twenty-two thousand miles above Earth Khan walks down the deck of his space station. The soldiers on the ship watch him as he carries Storm. Everyone on the ship knows Khan is just a man but they all revere him as a God anyway. Some can remember a time when Khan was a boy. Other people even laughed at Khan for his childish ideas of conquering dimensions; they do not laugh now. They all though have seen the way he cares for the common soldier and they also have seen him unmoved by a whole world burning. The strange thing about today, for his soldiers, is to see the same reverence they carry for Khan in his eyes for the person he carries in his arms.
On the ship's deck Tigio one of Khan's personal physician's is waiting along with the rest of his medical team. Tigio informs Khan that Storm has slashing wounds to the spinal column, significant neural trauma, and blood loss. Appearing through the transport beam Shaitan asks Khan not to save Storm's life. On bended knee, he tells his lord and commander that she is dangerous. Khan says that he hopes by saving Storm the other X-Men will try to rescue her, and walk into a trap. Next, Khan calls for a Skinwalker. One of his crew, Largo, wearing a protective containment suit pulls a vial out of a radiation labeled canister.
With his crew protesting, Khan takes the vial from Largo in his bare hands, and pours the vial of black goo onto Storm. She convulses as it surrounds her body. Mirroring her body, the controlled environment of the space station nearly creates a hurricane, accompanied by thunder and lightening. The hurricane and Storm's convulsions subside; telling Khan that she is fully imprinted. Under the orders of Khan, Shaitan leans over Storm's body and allows the Skinwalker to be transferred to his body. When the Skinwalker disappears, Shaitan no longer possesses his hulking alien form, but the body of Storm, with all her powers and her physical appearance. Gloating, Khan says he will use Shaitan in the guise of Storm to infiltrate the X-Men. Next he orders the physicians to restore the true Storm to perfect health because she is to be his queen.
In Madripoor Bishop attacks a cadre of aliens, taking them out by himself. When a ship flies overhead, firing at him, Bishop calls for back up. Thunderbird responds, shooting down the plane with an energy beam of solar plasma. When the plane crashes too closely, Bishop tells Thunderbird to be more careful. Meanwhile, the airborne Rogue fights three planes. As she takes out the three, she tells Bishop and Thunderbird that they do not need to worry about her, she is fine on her own.
While the three combat members of the team do their best to act like an army, the other newer X-Men deal with the collateral damage. Lifeguard finds a group of people trapped behind a fire. She asks them to grab her hand and then she tells Slipstream to teleport them away, which he does.
In a tunnel beneath Madripoor, Sage uses computer-like mutant power to eavesdrop on a conversation a trooper is having with his commander. The trooper requests authorization for the use of enhanced weaponry. Denying the request, the commander explains that until the tower is fully solid, only conventional weaponry is authorized. However, he will send in more troops to help. Near Sage's location in another tunnel, Viper hands out weaponry to the civilian populace. Forming guerrilla teams, Viper believes that if Madripoor is going down, then it will go down fighting.
Rogue appears with the other X-Men and asks Viper where Storm is. Viper tells them that Khan and Shaitan got the better of them both and she believes Storm's wounds might be fatal. Sage listens and remembers to herself that she saw Viper attack Storm, but decides to say nothing to the X-Men about it. Bishop asks Sage if she has any ideas to stop the enemy, to which Sage replies that actually, she has a few.
Elsewhere in the labyrinth of tunnels, Davis Cameron sits crying. Thunderbird finds him and tries to comfort him. Davis says that he thought being a mutant would be fun, but since he has become one he has done nothing but fight. Davis then says "and I can not ever go back". Thunderbird hugs him and points out that none of them can and says he is sorry.
Elsewhere, in a makeshift hospital, Lifeguard visits Red Lotus who had apparently sustained life-threatening wounds from his fight with Shaitan. He lays on a cot unconscious. As Lifeguard walks away, she passes Sage who has been watching her. Lifeguard stops to pick up the girl that she had saved earlier. Sage asks Lifeguard if she wants her to accelerate her mutant abilities to help stabilize her powers. Bitterly, Lifeguard tells Sage that unless she can take her brothers powers back away from him she will not allow Sage to play God with her mutant powers. As Lifeguard walks away, Sage thinks out loud that if she had done nothing, then what is going on in Madripoor now, would be the fate of the entire world.
Back on Khan's station he sharpens his sword, talking to it. He tells it how it soon will feast again. Storm wakes up in a luxurious room filled with attendants. The attendants wait on her, giving her a bath, dressing her, and feeding her. Very quickly, Storm realizes that her attendants are not simply servants but guards who are not only there to pamper her, but also to watch and record all of her movements. Storm decides to pull "a Sage" around her attendants: watching them, listening to them, and learning from them, but saying nothing.
Sometime later, Khan appears behind Storm as she stands in a flower garden. Khan explains to her that the nerves in her back were almost severed. The shackles that she now wears not only facilitate healing; they also provide constant telemetry on her condition, and her powers. Storm thanks Khan for saving her but asks why he wants her there. He tells her it is because he is a monarch, who desires a Queen.
In Madripoor's Lowtown, a soldier radios for help saying that he is under attack by new, stronger adversaries and he is the only one left of his crew. Just then Sabretooth, Wolverine, and the Hulk run to attack the lone soldier, but before they make it to him, the soldier faints. The illusion of the three foes fades, revealing Bishop, Thunderbird and Rogue. Bishop comments on how he actually felt as strong as the Hulk, to which Rogue says, thanks to her mix of telepathy and telekinesis, he was.
Bishop then comments to Rogue on her powers, as they seem to be under control a whole lot better lately. Rogue replies that she is just getting more of a handle on her powers. Through one of his teleportation portals, Slipstream arrives, bringing Sage and his sister, Lifeguard. Under the suggestion by Sage, the X-Men, except for Rogue, remove the armor from the unconscious soldiers and begin putting it on themselves. As the team suits up, Thunderbird looks at Sage and wonders if she did not have a part in Rogue's new handle on her on powers.
When, Rogue asks Bishop why she can't go with them; he tells her that they need her as back up. With the power and psyche of every super-being she has ever imprinted, Rogue's powers make her a one-woman army. He tells her that if they do not come back, she may have to kill Gambit to save the world from Khan's army. Rogue tells Bishop that she knows Storm is alive and asks Bishop to bring her man Gambit back to her.
In Khan's palace Storm reels at Khan's offer of becoming his queen. When she asks Khan if he expects her to live there shackled with the rest of his treasures, he tells her that he has found nothing that compares to her. As they dance, Storm tells Khan that if she means so much to him, then call off the invasion. Khan tells her no that he will win her world and then her heart. When Storm asks Khan why he is so arrogant, Khan replies that the worlds that embrace him prosper beyond their wildest dreams. When she asks what happens to those who resist, he grabs her by the neck and tells her that resistance is futile.
Back in Madripoor a group of soldiers find the X-Men disguised in armor. Believing them to be their fallen comrades, they pick the X-Men and request, by radio, immediate clearance to the portal.
Back on Khan's ship, Storm grabs Khan's hair violently. With his hand still around her throat, she tells him that she will never be conquered. After a brief moment of glaring at him she says that she can instead, choose... to surrender. With this, she pulls his face to hers and they kiss passionately.