On Madrizar, a Brood world, several Brood hunters have succeeded in capturing yet another Acanti – a female from the race of space whales they use as their living ships. They have already infected her with a slaver virus that is in the process of destroying her higher consciousness and sense of self-awareness. While the Brood discuss the fate of the escaped X-Men, they are suddenly surprised by the arrival of a very angry Binary who brutally slays the hunting party and outpost with her energy powers and then proceeds to free space-whale.
However, the Acanti telepathically tells her that it is too late, as the effects of the virus are irreversible. The only freedom left for her is death. Carol quickly kills the Acanti and then flies on, angrily thinking to herself how happy she initially was when she became Binary. But now, thanks to the Brood, there is only grief and hate left in her. She swears they’ll pay for that.
Carol’s suddenly called by Ororo who stands, without any protection, in space and asks her to join her. Carol is flabbergasted. She thought Storm and the other X-Men would either be dead or have changed into young Brood Queens by now. In a sense, she suffered both fates, Storm replies cryptically, and neither. When Carol asks how she can survive in space, Ororo answers that she in no longer quite the woman Carol knew and some of those changes were unpleasant.
This is merely an astral form, she explains and leads Carol to a young Acanti. Though no more than a newborn child, the space whale is huge. Carol admits that she just killed an adult of its species and Ororo assures her that it was the right thing to do under the circumstances. In fact, that adult was this newborn’s mother. They enter through the space whale’s mouth and Storm jokes that she won’t bite. She and the Acanti have become the same being, she explains. Within the Acanti they find Lilandra’s yacht. As they near the ship, they pass a membrane on one of the walls that covers a huddling figure barely recognizable as a human being. A legacy of one of her… more unpleasant moments, Ororo alludes.
Inside the yacht, they are expected by the X-Men, who crack some jokes about the way Carol left them. Kitty interrupts them; how can they be joking, since they are all going to die and there’s nothing they can do about it? They can do one thing, Wolverine contradicts her; make sure that the Brood don’t pull this stunt on anybody else. Should they attempt a suicide run on Brood World? The others argue. Storm interrupts hat they would accomplish nothing that way. She can, however, offer them a chance to stay true to their ideals and save lives instead of taking them.
She explains the history of the Acanti. They are peaceful beings that have been roaming space since the dawn of time. But then, the Brood, in many ways the Acanti’s opposite, showed up from God knows where. They considered the Acanti, with their ability to fly faster than light, their natural prey. Instead of building ships, they enslaved the Acanti and consumed them at the same time they were using them as ships. Among those Acanti captured on the first raid was their prophet singer, the Acanti’s leader and caretaker of their soul.
Normally, Storm explains, when Acanti die, they hurl themselves into a sun, essential in the case of the prophet-singer, for his body has to be completely consumed before the soul is released to be passed on to his successor. Without the soul, the race cannot survive. But when the captured prophet-singer died, the Brood turned his rotting corpse into their throne city, with the soul remaining trapped in the carcass. Hence, the Acanti cannot leave this part of space.
Recently, among the few survivors, a new prophet singer was conceived but, before the baby could come to term, his mother was infected with the slaver virus. She gave premature birth and the baby’s mind was too fragile to cope. It was about to die. That was when the Acanti found the dying Storm adrift in space. Bonding her into a physical and psychic rapport with the infant, Ororo provides that awareness and will to sustain the chid until his mind develops sufficiently. In return, its natural healing ability restores Storm’s body to health. Thus, for Ororo, a critical balance is re-achieved. She destroyed one child with the Brood embryo, now she can save another. What she has done for one, the X-Men might accomplish for an entire race. If they can release the soul, the child could lead the Acanti away to safety.
The soul, Ororo informs them, can be found in the head of the skeleton at its base. He’s been there, Wolverine interjects, some very nasty critters are claiming that turf. Peter and Kitty add that they’d rather die trying to fight for something than fighting against something. Scott agrees, but how to pull this off? He suggests that Storm and Binary create a diversion to draw the battle fleet, if possible, away from the planet. The others then beam down and make a run for the soul. By keeping the yacht inside the young Acanti, it is shielded from the Brood’s sensors. Wolverine suggests that he’d prefer it if he and Carol did the job on the planet while the X-Men stay with Storm. The three of them are the only ones who are free of embryos and might not turn on each other during battle. Angrily, Cyclops snarls if he sees things that way, he should cover himself before the mission. Finish them all off, then.
Wolverine hesitates. He can’t save his friends, shouldn’t he at least spare them the horror of the transformation? As Cyclops goads him, Wolverine unsheathes his claws, only to be stopped by Kitty, who tells both of them to put a sock in it. She tells Wolverine that they are not going to quit and part of that means that they have to stand together as a team. Wolverine backs down and Cyclops decides that they’ll be using his plan. Scott asks if Storm can use her weather powers in her current shape. She believes so, but it might prove a risk to her injured body. She tells Scott that she refuses to endanger the child but, apart from that, she’ll do what has to be done, whatever the cost.
A day later, the Acanti baby arrives on Madrizar. An interceptor squad tries to capture it but cannot match its speed, as the Acanti quickly heads for the skeleton and then flies upwards again. Storm tells the others that the Acanti elders approve of their plan but she is wrecked with doubts. If they fail, it will mean the destruction of all Acanti. Lilandra orders them to the transporter and Cyclops, being more tense than usual, insists Lilandra recheck her calculations. His rudeness doesn’t go unnoticed by Nightcrawler and Wolverine. While the others beam down, Ororo, steering the Acanti, leads the Brood on a merry chaser outside the planet’s atmosphere.
In the royal hive the Brood Queen is apprised of the situation. The hunt-master explains that they are chasing an Acanti newborn, but that they have noticed anomalies in its bio-scan. The Queen recognizes that they are signs of the baby being a prophet singer. Capture it and the Brood’s hold on the Acanti will be unbreakable. She warns them not to harm the child, when they are interrupted by the message of another Brood. The Queen does not recognize the newcomer, until it introduces itself as one of her children and betrays the X-Men’s plan. They are not aware that, in one of them, the embryo has already taken control of its host and is now telepathically communicating with the Queen. The Queen commends her daughter and orders the hunt-masters to assemble the finest warriors. She will lead them into the catacombs. The hunt-master is nervous about he prospect of entering the catacombs with its dangerous creatures but he’d rather face them than his Queen’s wrath.
In the meantime, the X-Men have arrived planetside, within the carcass of the dead Acanti, which smells even worse than it looks. No one is overly enthusiastic about entering this dangerous zone and Cyclops sarcastically asks Logan if he has “cold feet”. Wolverine takes the lead, pointing them downwards. Storm has keyed him telepathically in to the soul’s “scent.” He warns them that anything down there - whether plant or animal - is dangerous.
In the meantime, the enslaved adult Acanti ships are gaining on Storm’s infant Acanti. The Brood are already sure of their victory, realizing too late that Ororo led them straight to Binary, who shows them no mercy. Storm cannot bring herself to kill as well. Instead, she uses her mutant powers to stun the Broodships with lightning, painfully aware that this might damage her already injured human body beyond repair.
Meanwhile, in the catacombs, the X-Men have their hands full, fighting the creatures down there. Suddenly, Kitty is attacked by some protoplasmic being. Automatically, she phases and, in the process, passes through the wall as well, ending up separated from the others. Wolverine warns Cyclops that things will get worse the farther down, to which Scott gives a scathing answer. Wolverine is getting suspicious. They are being as hostile to each other as they used to be in the old days, except that this time, roles are reversed: Scott is the loose cannon and Logan the voice of reason. What’s wrong with them?
Kitty, in the meantime, has ended up on the other side of the wall and inside a huge nest with several eggs, one of which, she notices, is cracked open and has, therefore, hatched recently. She sees the bones of Brood skeletons in the nest, fairly recent kills at that, and decides she doesn’t want to stick around to meet whatever preys on them. As she uses her powers to slowly walk down on air, she isn’t aware that she has caught the interest of a hidden creature that’s following her.
In space, the Broodships have used tentacles to ensnare the stunned Binary and intend to infect her with the slaver virus. Storm wants to intervene but, when the Acanti child is hit, she is forced to flee. Like a deus-ex-machina, help arrives as the Starjammer materializes out of warp space, having recognized the energy signature of Storm’s powers – just in the nick of time.
In the catacombs Wolverine asks Cyclops where Kitty is. Cyclops mocks back; if he is so concerned, why doesn’t he go and look for her? Wolverine becomes more suspicious, especially as he notices that Scott’s shooting gets worse and worse, as if his body had forgotten the accumulated training of years in how to use his optic blasts. He catches his fellow X-Man’s scent, confirming his fear, and then attacks him. He tears away Cyclops’ visor, revealing Brood eyes underneath.
Scott’s already being controlled by his embryo and is working for the enemy. Unfortunately, the metamorphosis has given him control of his optic blasts and a wider firing range, which he quickly uses to take down Wolverine and Colossus. Lilandra and Nightcrawler plan to distract him but, at that moment, the Brood party catches up with them and stuns them. “Cyclops” asks the Queen whether he should kill Wolverine for her, seeing as how his embryo is dead. No, she wants the pleasure of killing and eating him alive herself. But for the services her daughter in Cyclops has rendered her, she will be allowed to partake in the meal. As soon as they have recaptured Kitty, they will return topside.
Kitty, in the meantime, is running for her life through the tunnels, chased by Brood hunters. Too tired to phase, she stumbles and the Brood catch up, salivating and telling her that if it weren’t for their order they’d eat her alive. Help comes from an entirely unexpected quarter: a deceptively, small purple dragon (who’s been following Kitty from the nest) spits fire at the Brood and quickly kills them. Having dispatched them, the little critter flies towards Kitty with a friendly grin. Both are attacked by another Brood –his shot misses and opens a hole in the tunnel’s wall, revealing a cavern. A beautiful light emerges from the cavern, mesmerizing and calling to Kitty even while the Brood screams in agony and the little dragon flies away.
Nearby, the X-Men have been shackled. The Brood are uneasy – the cadre that’s been hunting Kitty hasn’t returned yet. Cyclops suddenly bowls over in pain – his transformation is starting for real. With his optic blasts out of control Cyclops inadvertently hits the Queen. Wolverine realizes that this is his chance. Since the Brood have no eyelids, Scott cannot stop his beams right now (as he is too panicked and inexperienced in the power to consider blocking them with his hands). He jumps into the beam. While he is badly hurt as a result, he is still alive and his shackles are destroyed. Wolverine knocks out Cyclops, thus momentarily stopping the metamorphosis, and tells the soldiers to back off – or he’ll kill both the Queen and Cyclops. Reluctantly they comply and release the other X-Men.
After the X-Men have shackled Cyclops and the Brood, they follow Kitty’s scent to the radiant cavern. Kitty steps out, telling them that they needn’t worry about the Brood warrior that entered with her. He was judged by the soul and found wanting. He was turned to crystal before her eyes. Colossus is proud that Kitty wasn’t afraid, as she explains that she probably wasn’t affected as she’s still fundamentally human. She suggests they better leave the Queen outside and asks if anyone saw a little critter flying by. The Queen replies that they are flesh of her flesh. Were they go, so will she. The X-Men are amazed as they enter the glowing crystal cavern. They sense the soul welcoming them all, except the Brood Queen who feels hatred as strong as her own.
Horrified, Colossus notices that, beneath the Brood Queen, the crystal turns black. Her very presence is corrupting the place. As is the presence of her children, the Queen remarks, noting that the Brood-infected X-Men’s presence seems to have the same effect. As Wolverine orders them out, the Queen uses her back stingers to poison him, claiming that it is too late for them. Wolverine quickly “amputates” her fangs with his claws. As she boasts that he is about to die, he drags himself up with the rest of his strength. He sees with horror that the X-Men are all in the throes of their metamorphosis and that the empathic resonance of this event is saturating the chamber. The Queen boasts that the Acanti soul will be transformed with them and the Acanti will become one with the Brood. Wolverine drags himself over to Kitty intending to kill the X-Men and then, with his last breath, the Queen.
Suddenly, Binary flies down and picks him up. Logan asks her to forget about him: kill the others and save the Acanti, if she can. Below them, the Queen mocks that, even if they succeed, there is still a final royal embryo. When it hatches, their world is doomed. Carol ignores her and, remembering Storm’s instructions, she once more changes into her energy form. With her power being reflected by the crystal, she generates enough power to release the soul in a blinding bolt of energy that reaches the baby prophet singer.
An exhausted Carol checks on Wolverine. Both of them see with wonder that, as a parting gift, the soul purged the Brood embryos from the X-Men and transformed the Queen into crystal. Suddenly, however, the planet trembles and Carol assumes that this is her fault. She unleashed forces on a cosmic scale to release the soul. There’s no telling what kind of stress she put on the planet. She radios the Starjammers to beam them up, even while Kitty thinks about what will happen to her dragon. A few moments later, Madrizar explodes.
Some time later, in the Starjammer’s medical bay, the physician Sikorsky is giving Wolverine hell. He should rest and not get up. He was close to death. Wolverine, of course, ignores him. The others watch the exchange, amused at Wolverine’s stubborness. Scott admits to his father, Corsair, that the destruction of Broodworld bothers him, even though it wasn’t intentional. Corsair agrees that it should be hard to live with. He can only balance the deaths of the Brood with the countless lives they saved from them. They are joined by Storm who has finally been healed by the Acanti soul. The Prophet singer wanted her to stay, as, despite the soul’s presence, he is still very much a child… her child. However, she tells them, she didn’t want to leave the X-Men.
Both X-Men and Starjammers are in the mood for a big celebration, but the mood is spoiled by Wolverine, who tells them it isn’t over yet. Before she died, the Queen boasted of one last embryo that threatened Earth itself. He figures there can be only one person who could be hosting it. The embryo rests within Charles Xavier.