In Vancouver, Canada, young Sammy sits in the X-Jet, gripping the seat in fear as he overhears Professor Xavier's worry that the X-Men are in trouble.
The X-Men field team has crash-landed at Cassidy Keep and the unstoppable Juggernaut is bearing down on them. Archangel is injured, M is unaccounted for and Wolverine has been skewered. Nightcrawler and Stacy X try to save Archangel, who is not breathing, as Iceman steps from their crashed jet and blasts a beam of ice at the Juggernaut. After years of facing just such an attack, Juggernaut simply smashes through it and yanks out the pole that is sticking through Wolverine. Iceman ups the juice and blasts Juggernaut through the castle wall. He checks on Wolverine as Stacy and Nightcrawler try their best to revive Archangel, but before he can be saved, the ground bursts open and millions of vines wrap themselves around the fallen X-Man and pull him underground.
The Juggernaut comes smashing back onto the scene, easily busting through everything Iceman throws at him. The X-Men stand ready to face him, but Cain Marko reveals that he was the one who called them there to help. The X-Men are obviously confused and very reluctant to believe him, but they don't have time to argue with him. The vines come back stronger than before and rip the entire ground apart. Iceman and Nightcrawler escape, but everyone else is pulled underground this time.
At the Rosy Manor Convalescent Hospital in Upstate New York, attendant Annie Ghazikhanian is taking extra care of her most favorite patient, a young blond man with a scar across his eye, who is in an almost vegitative state. She pushes his wheelchair through the halls, and the other nurses feel sorry that this single mother of one spends all her time hoping this handsome young man will someday snap out of it and carry her off into the sunset. But then, at least she has hope.
She wheels John Doe out to the fountain in the yard. The only thing she knows about him is that sunlight seems to make him stronger. They meet her son, Carter, and look through the various magazines and newspapers they want to read. While glancing through the latest “Newstrack” she finds an article on the Xavier Institute. The article features a nice picture of two of Xavier's students, the Summers brothers Scott and Alex. The article says that Alex supposedly died trying to save people in a plane crash; it says that he is a mutant, and the picture looks an awful lot like Mr. Doe.
Back at Cassidy Keep, the X-Men have been dragged underground. The green vines are everywhere and they have captured many people, including the missing Monet, several unnamed people and also some animals. The vines wrap themselves around their prey and go up through the nostrils and in the mouth to suck the life from their captives. Wolverine, Juggernaut, and Stacy fight as best they can, and Juggernaut tells them that the vines are Black Tom. And speak of the devil, Black Tom appears to them, a man-shaped lump of the vines with beady yellow eyes. He yells at Juggernaut about how weak he has become, and how he has brought Tom's mortal enemies to help. It shames Black Tom, and he forces his vines into Juggernaut's face. Wolverine slices free and saves Juggernaut, and slashes at Black Tom's face. But the vines are everywhere, and Wolverine tries in vain to save Juggernaut and Stacy, as well as himself. He berates Juggernaut that the unstoppable one cares more for the man who's killing him than he does for his own step-brother Xavier, who had sent the X-Men into danger just to help.
Elsewhere is the castle, Iceman and Nightcrawler make their way through vine-covered halls searching in vain for their friends. Then Iceman reaches out and takes hold of one of the vines. He uses his moisture powers to draw upon the water within the vine. In a root system, the water would flow to the main trunk, and sure enough he's able to freeze the water and they now have a path leading them to the main trunk.
Back in Upstate New York, Annie makes a call to the Xavier Institute. Cyclops checks out her call on the answering machine, only to find out that his brother Alex might still be alive. His wife Jean is as surprised as Scott himself.
Back at Cassidy Keep, Iceman and Nightcrawler follow the trail of frozen vines and eventually find someone that looks like the new Black Tom. This creature utters in a most horrific way "get out". The walls crumble around them, and Iceman and Nightcrawler see all their teammates strung up by vines, their skin being sucked down to the skull.