She, along with Nightcrawler, was kidnapped by Dr. Doom and his Masters of Evil following his attack on SHIELD's Omega Base. While he used Nightcrawler to teleport into Mephisto's Realm to acquire the Twilight Sword, Jean was to be used to help destroy SHIELD's superhero team. Doom had Baron Mordo use his magic to redirect Stephen Strange's Orb of Teleportation to send the heroes to Murderworld rather than Doom's castle. There Arcade brainwashed Jean and used her to attack the heroes with hopes of unleashing the Dark Phoenix.
The heroes found Jean in her Dark Phoenix state, angrily claiming how everyone tried to suppress her power and proceeding to attack them. Distraught by her temporary defeat, she blasted the chamber in which she was fought, revealing that the heroes had actually wound up in Murderworld. She was later fought in the Big Top at Arcade's twisted theme park. Upon being beaten, he sucked her into a Pitfall! arcade machine, which the heroes had to beat to set her free. By doing so, they managed to bring Jean back to her usual self.
Returning with the heroes to Sanctum Sanctorum, she assisted Professor Xavier in scanning Nightcrawler's whereabouts, eventually finding him in Mephisto's Realm, to which he teleportated himself through the use of the Mutant Amplifier. She traveled there along with the heroes to try and keep him alive, since Xavier's telepathic link with Kurt was weakened by the realm's nature. But, by doing so, she fell prey to Blackheart, who abducted her and placed her in a cage high above the Infinity Vortex, as he had done to Nightcrawler before.
Upon defeating Blackheart, the heroes had to choose between saving Jean or Nightcrawler, in one last cruel ploy devised by Mephisto's son. Unable to save them both at the same time, the heroes are torn between two of their most loyal allies. Jean's outcome would then be one of the following:
- If Nightcrawler is saved, she will fall into the Infinity Vortex, but Mephisto will bring her soul back to battle the heroes. However, in one last glimpse of self-awareness, she will sacrifice her last sliver of life to defeat Mephisto. Later, after Doom's demise, she will rise again as the Dark Phoenix to get revenge on the heroes who didn't save her.
- If the heroes choose to save her, Nightcrawler will be hurled into the vortex instead, fight under Mephisto's control and sacrifice himself to defeat him. Jean then will be tormented with guilt of not being able to save her friend, and perhaps even more so after Mystique delivers a deadly blow to Xavier, resulting in his death and the X-Men's definitive disbandment.
Since it is shown that the X-Men have not been disbanded in Marvel Ultimate Alliance 2 it can be assumed that for this universe she is sacrificed but returns as the Dark Phoenix and is defeated and returned to normal. This is supported by her Dossier in Marvel Ultimate Alliance 2, as it states that Dark Phoenix has surfaced at least once in this universe.
In the aftermath of Lucia Von Bardas' attack on New York, Jean helped with the clean-up. She used her telekinetic powers to destroy some of the remaining Latverian Soldiers, as well as battling and defeating the Grey Gargoyle.
She was one of the many heroes to fight during the Civil War and subsequent war with the Fold. It seems that she has access to both her telekinetic powers, telepathic powers and cosmic pyrokinesis.
Seemingly those of Jean Grey (Earth-616)#Abilities.
Phoenix appears as a Non-playable character in Marvel: Ultimate Alliance for PlayStation 2, Xbox, PlayStation 3, Xbox 360, Wii, PSP, and is playable in the GameBoy Advance version of the game. She also appears as an unlockable playable character in Marvel Ultimate Alliance 2.