During a flight to Alaska, Jean Grey tries to psychically pinpoint the location of Charles Xavier, but fails when she feels another presence probe her mind and she discusses it with Scott Summers. Soon, another passenger begins raving about somebody else being is his mind, and the flight attendants arrange to get him a sedative.
At the Xavier Institute, the X-Men are cleaning up debris from the latest mess, as Archangel arrives, too late to see Scott and Jean off. He receives a very cool welcome from his teammates who feel he's not making an effort to be an X-Man, so he departs. Later, Sam Guthrie receives a letter from Tabitha Smith, and decides to join her at the "Colossal Man" gathering in Texas.
Back in the skies above Canada, Jean gets up to find Scott some aspirin to ease the pain of his recent surgery. Unexpectedly, A. I. M. agents board their aircraft and locate Dr. Sibelius, a scientist who has tried to elude them. They demand from him the location of "the entity", but they stun him when he refuses to cooperate. The entity then begins to probe the minds of those aboard, and they are forced to recall traumatic memories.
Jean enters the cargo hold to find the "entity", and locates it in an armored container set to explode if tampered with. Mentally, she communicates with it, learning it has been held captive and tortured by A. I. M. scientists. She has to hide when the A. I. M. agents escort Sibelius' companions into the hold to find the "entity". Again, the "entity" invades the minds of all aboard, and the plane's wing collides with the A. I. M. cratf which plummets to its doom. In the confusion, Scott tackles the agent guarding the cockpit, while below, Jean decks the one agent left standing. She again reaches out to the "entity", and begs it to calm the crew and passengers so the plane may land safely, and it complies.
The aircraft comes to an emergency landing in Manitoba, and Department H agents take the container holding the "entity" into their custody.