Several Brood scientists subject their captive, Carol Danvers, to an evolutionary modification ray, which continuously changes her inner and outer appearance. Carol intrigues them, not only because of the indomitable willpower she shows in the face of unbearable pain, but also because she is neither baseline human nor mutant like the X-Men.
One of the scientists sends another Brood to get refreshments. The Brood is unaware that he is being followed by Wolverine, who gets into the lab with his unwitting help. Wolverine quickly kills all the Brood in the lab and then sees Carol on the slab - no longer recognizable as a human being, her features flowing like wax.
Havng no idea how to turn the machinery off, Wolverine hopes for the best and simply destroys it. He is lucky - Carol looks once more human, although both of them sense that this is no longer the case. Nevertheless, they have a job to do. Carol grabs a robe and one of the Brood's guns and thanks Logan for saving her life for the second time. She wonders how odd it is that, after an ordeal like this, she feels as though she were bursting with energy. Together, they go to find the other X-Men.
Meanwhile, back on Earth, where Shi'ar drones are busily reconstructing Xavier's mansion. Corsair and Havok are being beamed down from the Starjammer to find Polaris and Moira MacTaggert waiting for them. The news is grim: Lilandra and the X-Men have been kidnapped. The Shi'ar Empire is embroiled in civil war as everyone's choosing sides between the missing Lilandra and the usurper Deathbird, who has allied herself with the Brood, aliens from beyond known space. The price of the alliance was the X-Men. The Brood have taken them to their homeworld and no one knows where that is.
Alex angrily lashes out with his powers at some girders, as he feels helpless. Corsair, hearing the energy bolt, reacts automatically and presses the phasing jewels on his gloves to summon his blasters. As he realizes that this was just his son blowing off steam he lets the weapons vanish again. He's a bit nervous, Moira notes. Corsair outlines his plans: the Starjammers are going to search for the X-Men, to rescue or avenge them. He doesn't want Alex along, though. At least one of his sons should be safe, besides he doesn't want Alex to become a killer. They'll be leaving soon, he tells Moira, after saying good-bye to her and Xavier. Moira notes that Charles isn't there. He's taking this very hard. Losing the woman he loves and his beloved family - the X-Men - in one stroke might break him. She wishes Corsair good luck as he is beamed away.
A galaxy away, Scott Summers is caught in a nightmare. Finding himself in an alien jungle, he is running for his life from an endless number of Brood warriors. He suddenly sees his fellow X-Men standing on the other side of a river, shouting for him to join them. He runs towards them but, when he arrives, he is greeted by Brood, in the X-Men's clothing, calling him "sister". When he shouts, asking what they have done to the X-Men, they reply, "we are the X-Men". Cyclops blasts them in horror and denial with his optic beam. Suddenly, a Brood, in his own costume, informs him that denial won't help - his fate is sealed. It tells Scott that a Brood egg has been implanted in him and soon he will become Brood.
The X-Men-Brood savagely tear at him, trying to strip away his humanity, when suddenly giant hands brush away the Brood and lift Scott up. He sees that they belong to a giant version of Professor Xavier and begs him for help - he's going insane! Xavier sternly reminds him that such help was already given with his training. Scott realizes that Xavier and all the other images are only phantoms. He uses his training to resist psychic attacks, until he finally awakes and the dream flees from memory.
Looking outside, Cyclops realizes that this alien world looks nothing like the Shi'ar throne world from Xavier's descriptions. He notices Ororo outside, kneeling in a trance and decides it would be better not to wake her. He wonders about their clothes being in tatters. How does that fit with his memory of the party and why does his nightmare indicate some sort of psychic conflict? Are they being manipulated? Suddenly, he sees a phantom image of a Brood coalescing in front of the meditating Storm. It smiles at him, lightning splits the sky and the image fades. Ororo, still in her trance, is crying and Scott wonders if she's suffering a similar nightmare, so he wakes her.
Ororo doesn't know why she was crying, only that she is at war with herself and doesn't even know why. Scott gives her a comforting hug, while wondering why he is so defeatist. He feels as though they had already lost and doesn't understand why. They are joined by Wolverine and Carol, who tell them that getting away from the planet is currently their first priority. Logan suggests swiping Lilandra's yacht, which is just above the breathable atmosphere, docked on the exposed rib of the Brood's now-dead, living starship. They get the other X-Men and, very soon, a team consisting of Carol, Wolverine, Cyclops and a still disbelieving Colossus goes scouting the tunnels of the Brood palace for Lilandra. Cyclops wonders about Wolverine's scaly skin and what is bothering him.
Carol notes that the corridors seem to be part of a natural organic process rather than constructed, whereas Colossus admits that he still perceives a normal metal hallway. Wolverine wrestles with his conscience: should he tell Cyclops and the others about the Brood embryos implanted in them? Fortunately, he is diverted as the tunnels branch off. One of them leads to Lilandra's holding chamber, the other to the Brood Queen. Wolverine demands that they kill her - it would cripple all the Brood. Cyclops refuses. That's not why they're there. Angrily, Wolverine retorts he's has enough of Summers' boy scout rules. This is war! Carol interjects that they had better postpone their discussion, as they have company - the "armed Brood warrior kind of company". The Brood leader orders his people to harm the X-Men as little as possible. The battle is joined, while Cyclops wonders about the Brood's reluctance to harm them.
With the X-Men keeping the Brood busy, Carol runs to spring Lilandra. Cyclops and Wolverine start another argument about killing the Brood Queen. Wolverine is determined to finish her and faces her. The Queen is furious. She senses that the embryo implanted in Wolverine has died. Over the other X-Men's protests Wolverine closes in on the Queen, while Brood reinforcements arrive. Thankfully, so does the cavalry in the form of the armed Carol and Lilandra. Carol suggests a strategic withdrawal, but Wolverine is determined to finish what he came for. Cyclops threatens that he'll carry him out if need be. Wolverine is endangering their lives! Logan cryptically replies that they are as good as dead anyway, thanks to the Queen. Killing her will, at least, balance the scales. He'll stay!
Meanwhile, high up in the air, Storm is using her weather powers to fly herself, Nightcrawler and Kitty as high up as possible - not an easy task considering she feels something is very wrong with her. She flies them as high up as she can, but they are still miles below the yacht. Nightcrawler teleports himself and Kitty away, while Storm is left to deal with the Brood patrol and buy her friends time.
Nightcrawler and Kitty arrive on the outer hull of the yacht and Nightcrawler wonders why his power is putting a far higher strain on him than usually. Kitty phases inside to find an airlock. Unfortunately, she's surprised by a Brood guard ordering her to surrender. Kitty avoids the Brood's stinger attacks, painfully aware that the longer she takes, the higher are the odds of Nightcrawler asphyxiating or freezing to death outside. Recalling everything she's learned from Xavier about Shi'ar ships, Kitty plans to close the inner hatch and then open the outer one, allowing Kurt to come aboard. Unfortunately, the Brood's fast enough to slide into the airlock chamber with her.
Kitty's unsure what to do. She could open the outer door by pressing a button, thus allowing the decompression to suck the Brood outside, while she'd simply phase, but she can't bring herself to commit murder. The Brood breaks the standoff by attacking her. Kitty phases, the Brood slides through her and accidentally presses the button, opening the airlock. The warrior is sucked outside. Kitty drags the unconscious Kurt on board, while thinking to herself that Wolverine would applaud her for causing the Brood's death, but she doesn't want to become like Wolverine.
Meanwhile back on the planet, the fighting X-Men wonder, if anything's gone wrong with Kitty and Kurt. "Murphy's law," Wolverine sarcastically states while poising himself to strike at the Brood Queen. Something always goes wrong. The Queen dares him to strike, claiming that her death will not be a true death. In the end, she shall triumph. Cyclops orders Wolverine to stop, while Lilandra calls him a fool for that - in a deadly war there is no place for chivalry or honor. Logan agrees. Just as he wants to kill the Queen, all the X-Men are beamed away up onto Lilandra's yacht. Now at full thrust, the Z'reee Sh'ar leaves Broodworld behind it.
Lilandra cautions the X-Men though, that they are still too deep within solar gravity to shift into warpspace. They are still vulnerable and while the yacht s armed, it s no match for the Brood warships that will no doubt be waiting for them.
Wolverine, in the meantime, rants at Cyclops. He'd only needed a few more seconds. Had Scott backed him up from the start, the Queen would be dead. Kitty asks him why he's so mad at the Queen. Wolverine doesn't know, how he can tell his friends what terrible fate lies in store for them. As Wolverine begins to answer them, he and the rest of the X-Men are unaware that their vessel is in the cross hairs of another ship, preparing to attack.