The Watcher recalls the tale of the Phoenix. A young woman, Marvel Girl of the X-Men, sacrificed her life to save her team mates while they were in space. The Phoenix Force came to her aid and as a result, she became Phoenix. Phoenix saved the galaxy from Firelord and D’Ken. Frightened of her immense powers, Phoenix “set up a series of psychic circuit breakers to contain it”, but she was eventually corrupted by Mastermind of the Hellfire Club, and she turned into Dark Phoenix. While the X-Men were able to temporarily bring her under control, the Shi’ar delivers Phoenix her death sentence, leading to the battle on the moon where Marvel Girl commmitted suicide to save the galaxy from the Phoenix.
The Watcher then tells the tale of an alternate universe where change in the turn of events leads to a different outcome. In that very same battle, a blast meant for Cyclops that defeated him, hit Marvel Girl instead. Enraged, Cyclops as the last X-Man standing keeps fighting until he is spent and surrenders. Phoenix is left to be dealt with by the Shi’ar. The Shi’ar chooses to lobotomize Marvel Girl, thereby imprisoning the Phoenix, but also taking away Jean’s powers. Jean returns home, a shadow of her former self.
Without her powers, Jean is forced to retire from the X-Men. She turns to housekeeping chores to ‒make [herself] useful”, which saddens Beast and Cyclops to see her “so docile”. Beast and Angel, who are no longer full-time members of the X-Men, take their leave.
The X-Men continue training as usual, and takes in a new student, Kitty Pryde. Jean misses her telepathy, and even an urgent telepathic summon from Professor Xavier is a welcome sensation. Xavier was contacted by the Shi’ar requesting help from the X-Men to defend the planet Arama, which has come under attack by Galactus, a god-like being who feasts on the energy of living planets. Cyclops is upset that the Shi’ar had the nerve to approach them for help, but Jean defends the Shi’ar’s decision to stop the Phoenix, and that should not stop the X-Men from helping to save lives, knowing what Galactus will do to Arama.
The X-Men set off for Arama. Jean and Kitty are ordered to stay in the Starcraft for their own safety. Jean watches in disappointment as the X-Men head into action. She feels helpless and unable to help the X-Men without her mental abilities. Suddenly, her psyhic rapport she once shared with Cyclops awakens within her when she senses his life in danger. Once again, she becomes Phoenix and defeats Terrax, Galactus’s herald who attacked Cyclops. Phoenix then seeks out Galactus. Galactus makes her an offer to join him as his new “herald” Knowning she is not a match for Galactus, she destroys his “planetary conversion device” instead, and Galactus retreats.
The X-Men are awed by Jean’s renewed powers as Phoenix. The people of Arama are grateful to Phoenix for saving their lives. Even Lilandra, empress of the Shi’ar, offers her gratitude. Phoenix hopes she has “made amends for the destruction of the star, D’Bari”.
In the months ahead, the X-Men are “nearly invincible” with Phoenix on their team. Cyclops is happy that “the woman he loves is whole again”. But unknown to everyone, Jean fights to control her Phoenix powers completely so as to ensure the Dark Phoenix never emerges again. It is Kitty who notices one night that Phoenix has slipped out. (She had travelled into space to consume some asteroids to sustain herself.)
Another fierce battle with the Sentinels where Phoenix singlehandedly defeats the Sentinels drains a lot of her power. Under the guise of flying herself back to the mansion, Phoenix escapes into space and consumes a “small star with no inhabited planets”.
Unbeknowst to Phoenix on her return, Xavier had been monitoring her activity since Kitty had suspicions about her sneaking off into the night. Kitty confronts Phoenix about destroying the star, and in a fit of rage, Phoenix kills Kitty. The X-Men are shocked.
Xavier tries to stop Phoenix but even his mental powers are not a match for hers. Phoenix renders him brain dead. The rest of the X-Men attack Phoenix and are subsequently killed. When Phoenix kills Cyclops’ brother Havok, Cyclops decides he has had enough. Regardless of how much he loves Jean, he cannot let her continue on her murderous rampage. But he is unable to stop her and is killed.
When Phoenix realises what she has done, fury consumes her and she destroys Earth, and “everything in its path”.