This episode begins where the previous one leaves off. Jean Grey is struggling to maintain control over the rocket, while also using her mental powers to shield herself from the harmful radiation through which the spaceship is flying. After passing through the radiation, Jean crash-lands the rocket in the middle of the Hudson River.

As the X-Men and the ship's crew escape from the destroyed ship, Jean Grey flies up out of the water and claims to be something called "Phoenix". Jean is brought to a hospital to rest, and the X-Men later question her about Phoenix. She has no idea what is going on.

Cyclops stays in the hospital with Jean while the other X-Men venture out into New York City. Gambit and Jubilee head to see a Broadway show. Beast goes to his Manhattan research lab in order to investigate the mind-control chips that were placed into the space station's crew by Erik The Red. Storm decides to meditate on top of a bridge and Wolverine heads off on his own.

Professor Xavier is seen on the roof of the hospial and starts getting into his personal hoverjet, when he again sees visions of the strange alien woman who has been hauting him for the past few days. The mental contact between the two puts Xavier into a come-like state, and his mutant telepathic abilites begin to project his astral form outside of his body.

His astral form, which it later becomes apparent is really the "evil side" of his psyche, confronts the X-Men one by one. The astral form meets up with Wolverine on a subway and plays mind games with him. However, Wolverine's mutant ability to distinguish people by their unique smells tips him off that the astral ghost is not really professor Xavier and that something must be wrong. Wolverine finds Gambit and Jubilee on Broadway, just as Xavier's evil astral form is attacking them, and lets them know that it is not really the professor. The three of them try to battle the ghost, but with little luck. Jubilee contacts Storm for assistance. To the police officers, to whom Xavier is not revealing his psychic presense, it appears as though the X-Men are just causing damage for no reason.

As the cops are about to arrest the X-Men for vandalism and destruction of property, Storm comes to their aid just in the nick of time. She creates a dense fog, allowing the four of them to escape.

Xavier's astral form next attacks Cyclops, in Jean Grey's hospital room. Jean tells Cyclops that it is just an astral projection of Xavier's dark side and that he has to realize that whatever "hurt" Xavier's projection might be causing him is all in his head. Cyclops cannot fight the projection though, so Jean Grey uses her own telepathic powers to force Xavier's mental projection away.

The X-Men rush to assist Xavier's physical body. Upon waking him up, Xavier apologizes and explains that his hauting vision of the alien overwhelmed his powerful psyche, causing his evil subconscious to lash out at the X-Men. He told them that he could not be trusted in his precarious mental state, and traveled to Muir Island, Scotland, where his good friend and scientist, Dr. Moira McTaggert could properly and safely tend to him.

Moira, a former love interest of Xavier's, introduces Professor Xavier to her new fiancee, Sean Cassidy. Meanwhile, Erik The Red is seen utilizing advance alien technology to spy on Xavier and overhears him mention the alien visions. Erik The Red says something about Xavier being "the key" and needing to deal with him. While sitting alone, Xavier gets another violent vision of the strange alien woman.

He mentally reaches out to her this time, rather than fighting to resist her presense. This causes her to show up in front of him. She reveals herself as Lilandra and explains that she is from an alien galaxy called the Shi'ar Empire. Her brother, D'Ken, is the emperor of the Shi'ar people, but he is corrupt. His biggest wish is to use the incredible powers of something called the M'Krann Crystal in order to rule over the universe. Knowing this, Lilandra stole the M'Krann Crystal and fled her planet for earth. According to Shi'ar beliefs, two people are bound together from birth and destined to find each other in their times of need; for Lilandra, this person has always been Charles Xavier. As if to confirm this belief, the two each feel as if they've known the other for years despite having just met and immediately begin to become close.

The episode ends with Xavier's greedy step-brother, Juggernaut, breaking into the room and grabbing Lilandra.