Amphibius swims through the cold waters in search of his master, Magneto. He finds Magneto barely alive, and drags him to the nearest shore.
On Muir Island, Professor Xavier and Doctor Moira MacTaggert are running tests to find out what happened to Jean when she was out in space. They cannot find any residue of the effect. Moira’s only suggestion is to “keep any eye open for any reoccurrence”.
As Jean gets changed for her return to the Institute, Moira comes to talk to her. Moira inquires further about Jean’s experience. Jean can only go as far as explaining what she felt. Jean also confides in Moira about her troubles regarding Xavier. He had lied about taking her to see some specialists in Boston. Moira explains that they have to keep the Muir Island facility a secret from evil mutants. Still, Jean is unnerved that the Professor would only share secrets with her, and not with the rest of the X-Men.
On the jet back to the Institute, Jean confronts Xavier. Xavier explains that they are both telepaths and are able to shield their minds against probes while the other X-Men can’t. The deceptions still doesn’t sit well with Jean. Returning to the Institute, Xavier is immediately informed by Cyclops and Beast that Cerebro had detected a new mutant.
At the residence where Cerebro detected the mutant, Ashley’s behaviour makes her mom suspicious. She was awake earlier than usual and in the barn.
Xavier and Hank prepares for a trip to Illinois where Cerebro had detected a mutant. Xavier had fitted a portable Cerebro unit in the vehicle, but he isn’t able to pinpoint the exact location due to the presence of “some kind of conflicting signal”. They make a stop at Hank’s home to visit his mom.
Meanwhile, back in the Institute, Scott and Jean work on Cerebro to track down Warren’s whereabouts. They are interrupted by Candy Southern. A quick glimpse into her mind tells Jean that Candy is well aware of the X-Men. Candy explains that Xavier had allowed her access into the Institute.
In the Savage Land, Havok, Magnetrix and Ka-Zar rush to Iceman’s location. Bobby is still unable to remember anything. He watches as his saviour and mortal enemy Sauron fixes some equipment. But Sauron remembers well why he had come to the Savage Land. He sought isolation where he could hurt no one, especially the woman he loves.
Xavier and Hank arrive at the house where Cerebro had detected the mutant. When no one responded to the doorbell, Hank scouts the area. Hank too is unnerved by Xavier’s change in behaviour after recovering from his coma, treating them like “neophytes”. Hank follows the trail of toys to the barn.
Cyclops, Marvel Girl and Candy dressed in Marvel Girl’s current green and gold costume are in the jet flying to rescue Warren. The coordinates bring them to a freight ship. Cyclops, Marvel Girl and Candy board the ship and are ambushed by the ship’s crew. Cyclops notices that they are working to keep them from entering a certain door, and the three manage to barge their way through the door. Cyclops makes good work of locked doors with his optic blasts. They find one of the captives in a holding cell.
Ashley returns home to find Professor Xavier in her front yard. At that moment, Hank is attacked and thrown out of the barn by the Sentinel hiding in it. Detecting more mutants, the Sentinel attacks Xavier and Ashley as well, under the command to “destroy all mutants”.