Jean Grey and the X-Men fought the Shi'ar Imperial Guard on the Blue Area of the Moon for her life, after the Dark Phoenix had destroyed the D'Bari Star System and a Shi'ar battle cruiser. Unfortunately, the X-Men lost the battle, and they were taken to flagship of the Shi'ar fleet where Cyclops was unable to prevent a psychic lobotomy being performed on Jean which destroyed the portion of her brain that her mutant powers resided in the hopes of containing the Phoenix force within her.
Jean and the other X-Men returned to the school, and she almost immediately took on a docile role of servant in an attempt to fit into the school once again. However, everyone pitied her for the loss of her highly spirited nature, but she soon began training the others to use their mutant powers more effectively, especially young Sprite who had just arrived at the school to begin her training.
Later when Lilandra Neremani telepathically contacted Professor X for the X-Men to save a planet named Arama from being destroyed by the planet eater, Galactus, Cyclops voted against it due to the actions of Lilandra towards Jean. Jean was shocked by his reaction and demanded that the team do what it could to help the doomed race, once again showing her spirit of justice.
As the X-Men fought Galactus' herald, Terrax the Tamer, he struck them all down, almost killing Cyclops, which awoke the Phoenix Force inside Jean, transforming her once again into the Phoenix. She soon joined in the battle and soon stripped Terrax of his portion of the Power Cosmic leaving him only a naked broken man. She then attacked Galactus directly and eventually drove him from the planet, saving the Aramans in the process.
Soon, the X-Men returned to their normal lives, however, Jean eventually began to lose control of the Phoenix force once again, which horrified the other X-Men. As they confronted her over her consuming a star without any inhabited planets, Jean transformed into Dark Phoenix and battled the X-Men and killed each of them one at a time.
Kitty Pryde was the first to reach Jean Grey who confronted her about she had done, transforming her into Dark Phoenix in the process and struck out at Kitty, turning her into a pile of dust in the process in front of the eyes of the other X-Men. Colossus was heartbroken at her loss, as he had never told her how much he cared about her.
Professor X attempted to psychically contain the Phoenix Force in Jean's mind as he had done once before after she had transformed into the Black Queen of the Hellfire Club. However, the Professor was unable to overcome her formidable psychic presence a second time, and the Dark Phoenix reduced him into a vegetative state.
Next, the Angel confronted Dark Phoenix and begged her to listen to them. Instead, she flung him head first into a brick wall killing him on contact, without a second glance as she turned her attention to Storm. The Dark Phoenix remembered that Storm was claustrophobic so out of cruelty, dug a hole in the ground and buried her alive while at the same time she encased Iceman into the same brick wall she had bashed Angel into moments earlier.
The Dark Phoenix knew of Nightcrawler's devote Catholic faith and so in accordance with church doctrine, she created a pyre of hellfire and threw Kurt onto it, burning him alive without his ability to teleport away to safety. As Colossus threw Wolverine at her with their Fastball special she stopped it and threw it back at him, but transforming Colossus back into a flesh and blood human first. He was killed as Wolverine's claws went through his heart. After being forced to kill Colossus, Wolverine didn't fight when he was thrown into the same hellfire that burned Nightcrawler.
With the last three X-Men still able to attack, they quickly formulated a plan where Polaris would distract her as Havok and Cyclops flanked her ready to take her down to save the world. Dark Phoenix proved to be quicker than they anticipated, and Polaris was reduced to ashes in the same manner Sprite had been which prompted Havok to attack prematurely and Cyclops to hesitate. That moment's hesitation cost Cyclops dearly as she telekinetically blew a hole in Havok's chest, killing him slowly.
With only Cyclops and Dark Phoenix left, and though he still loved her very much, Cyclops attacked Dark Phoenix the his most powerful optic blast, which she shrugged off and blasted him full in the face, killing him instantly. His death resulted in Jean's personality regaining control over the Dark Phoenix and going mad with her grief over what she had done.
After all the X-Men were dead, especially her lover, Cyclops, the Dark Phoenix persona became dominant and eventually destroyed the entire universe.