In Westchester, New York, at the Xavier Institute, Bishop and Professor X discuss whether or not Cerebro is ready to be used once again after Banshee was forced to destroy it, lest it be fall into the evil hands of the Phalanx. With a confidence stemming from his months of testing his new machine, Xavier declares it ready for its first test. The Professor is immediately shaken with the discovery of an enormous energy spike in northern New Jersey, which he attributes to a malfunction of the new machinery. Bishop, not one to take chances, runs off to gather the only other available X-Men: Beast and Gambit.
The three X-Men arrive at their destination’s coordinates via the Blackbird, only to learn their target is actually a commuter train. They drop from their aircraft onto the fast-moving conveyance. Beast’s sense of adventure is not impressed, as he cracks jokes about what 3rd rate villain they are doomed to meet on this particular adventure. Perhaps “Abacus, The Mutant Accountant!?” Gambit, in his usual suave manner, quickly charges a few playing cards and creates a makeshift entrance to the last car on the train.
The heroes’ confidence is wiped from their expressions when they enter to find a practical wall of highly mutated and deformed monsters, screaming for help! Bishop, taking on the role of temporary leader, quickly deduces that the current situation is what caused the Cerebro spike: “a trainful of people - mutating wildly!” While Beast attempts to analyze the situation out loud and wonders what could have caused it, Bishop and Gambit spring into action to accomplish their goal of saving the remaining humans.
Beast, attempting to save a woman huddled in a corner, is taken back as she screams in horror at his attempt. While Beast assumes she has confused him with the deformed mutates, Gambit realizes the real reason she is so afraid, as he witnesses one of the mutates grab a human, only for the human to be transformed into a monster as well through skin to skin contact. The three X-Men realize together how much more serious their situation is; whatever is causing the rapid mutations is contagious.
(Annandale, New York)
At the home of Jean Grey’s parents, Scott Summers quizzes his new niece and nephew with a simple game of “which hand is the coin in.” As Jean’s parents revel at “how good Scott is with the kids,” Jean is absent-minded. She is more concerned with what Cyclops is really doing. She excuses herself and goes on to scold Scott for “testing” her relatives for mutant powers. While Scott believes it to be for their own good, Jean has very different ideas about the situation. She convinces Scott that it would be better to let them grow up and have their own childhood. Jean asks if it’s possible for Scott to stop worrying about the fate of mutant-kind long enough to enjoy a day with their family.
Their romantic moment of teasing is interrupted by Jean’s father, saying they should watch what just came up on the TV. It seems Graydon Creed, a mutant-hating bigot, is announcing his candidacy for president of the United States. The room is in a communal state of worry, as Jean wonders whether or not the Professor has heard.
Professor X makes a phone call to the office of Ambassador St. Croix. They worriedly discuss the implications of Creed’s bid. St. Croix observes that Creed is even more dangerous and threatening than Senator Kelly used to be. His organization, Friends of Humanity, exists solely to fan the flames of anti-mutant hysteria. Xavier is one step ahead. He asks the ambassador if the “underground mutant network” is still in place in case his students need to take drastic measures.
Back aboard the train, the X-Men stay together and avoid contact while attempting to devise a plan to stop the train before it hits New York City, along with the plague it’s carrying. Bishop says he does and purposely takes an energy blast from one of the mutates, so that he can redirect it through the ceiling to create an exit. He takes Gambit with him and charges Beast to stay behind and find a way to subdue the passengers. They decide to head for the engine, to stop the train once and for all.
Gambit and Bishop aren’t so lucky in finding the engineer unaffected and run into heavy resistance in the form of a very large and powerful mutate. Beast, meanwhile, is not happy about his assignment, but still has a plan in mind. Rattling off various chemical ingredients, he makes him way through the train collecting bottles. He realizes he needs something from below the train and baits one of the mutates into attacking, creating a hole in the floor of the speeding train. Underneath the train, he begins searching for brake fluid to complete his makeshift plan. Gambit decides he can handle the monstrous mutate, while Bishop heads for the controls of the train, only to find they have been shattered and rendered useless. Gambit, worriedly staring at the oncoming tunnel, advises Bishop that if he doesn’t do something soon, “dey’ll be scraping us outta de tunnel wit’ a spatula!”
Beast has since mixed his ingredients to make a knockout gas of some kind. He fills the car with the gas, and the few mutates that aren’t affected, he kills himself. This shocking departure of character is due to a deep, dark secret that none of the X-Men are aware of. Hank McCoy, the fun-loving Beast, has been replaced by a malevolent doppelganger from another timeline, a secretive schemer whose primary objective is to remain hidden from one certain man. Beast’s gas, while relaxing and knocking out the passengers, also changes them back to human form as their bodies relax.
Beast is then approached by Mr. Sinister, who claims responsibility for the plague and expresses his fury towards Beast for stopping his experiment. Sinister grabs Beast by the throat and intends to head through the train to meet “whoever he may have brought with him.”
Bishop, rejoining Gambit, knocks the extra large mutate clear off the train, buying the two heroes enough time to think, at least momentarily. Since they agree they can’t derail the train, for fear of killing everyone aboard, Gambit decides to take a chance with something he doesn’t have time to explain to Bishop. Gambit chargers the entire train with kinetic energy. Bishop is furious, yelling at his teammate: “Things were bad enough before! Now-- we’re riding a thousand-ton bomb -- STRAIGHT INTO THE HEART OF MANHATTAN!”