Government agent Stephen Marchesi has come to the Nest, a secret government nuclear testing facility located in the Pahute Mesa region of Nevada, where a team of scientists are working hard to try and find a solution to the world's dwindling energy resources by finding alternative energy sources. Among the scientists are Brian Mann, the nuclear physicist in charge; Vic Norman, a bio-physicist; Jan Maarshall, an electrical engineer; Karen Lee, a geologist and Marchei's ex-wife; Si Fan Chung, an Astronomer and Karen's new lover; Martin Aaronson a radiation expert, and Randy Tate the project overseer and former flight attendant. As they are testing out a new experimental form of radioactive energy dubbed the Nila Pile, an sudden earthquake disrupts the experiment, shattering the containment glass and causing an explosion seemingly killing everyone as the facility explodes in a massive nuclear explosion. The project was canceled by the government shortly thereafter.

Months later a Boeing 474 is flying over the Arizona desert on its way to the International Conference on Man-Made Mutation. Aboard the plane are noted scientists Sir Lionel, Dr. Fermizi, Dr. Mishkin, and the outspoken Senator Turner. Turner is in a fury not only because a Soviet Dr. Miskin is aboard the plane, but because accompanying Professor Charles Xavier, are his students, who managed to get a free flight on Reed Richards' say-so. Professor Xavier defends his students' presence aboard the plane to all gathered there, including Peter Parker, who has been selected by Sir Lionel to cover the story for the Daily Bugle due to Parker's background as a physics student. Things become heated when Wolverine begins to pick a fight with the Senator.

However, things get hairy when they fly through a dark cloud and suddenly they are attacked by the robots that once defended the Nest. As the X-Men rush to fight off these robots, the Professor orders Cyclops and Colossus to try to control the plane after the pilots are incapacitated. Recognizing some of Xavier's students as the X-Men, Peter slips away to change into Spider-Man and lend a helping hand. He almost has his identity blown when he forgets to lock the bathroom door and Senator Turner bursts in to be airsick.

Spider-Man aids in fighting off the robots, and when he learns that Cyclops can't slow the plane down for a safe landing, creates a web-parachute to slow down the plane so that Scott can land it. In trying to make sense of the situation Dr. Mishkin pulls out a radiation detector and identifies that there is a lethal amount of radiation coming out of the blast crater where the robots appeared from. Spraying Spider-Man and the X-Men with anti-radiation spray to make them immune to the effects of the radiation, the Wall-Crawler and the X-Men go in for a closer look.

As they approach the crater, Professor X attempts to warn them of danger, but he is too weak following recent ordeals[2] to warn them full of the danger. When Storm and Banshee fly in first, Spider-Man is concerned about whether they can face whatever might be waiting for them in the crater, which angers Wolverine enough to almost start a fight between the two. Before a fight breaks out they are disrupted by an earthquake, and down below Banshee and Storm are felled by some unseen hands. The X-Men on the surface are then attacked by a being calling himself Yama Dharma, who then attacks them. During the fight, Wolverine slashes Yama's chest open and is shocked to find a strange cosmos spinning around inside. Soon after, the X-Men and Spider-Man are all knocked out by Yama and his colleague Kali. With the X-Men and Spider-Man knocked out, they isolate the one they sensed, Jean Grey.

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