In the timeline known as the Days of Future Past, Jean died when Mastermind detonated a nuclear device in Pittsburgh, though not after she had given birth to her daughter Rachel a few months before. There are conflicting reports whether this Jean too had been replaced by the Phoenix Force or not. Likewise it was not quite clear who the father of Jean’s daughter was; whereas Rachel considers Scott Summers her father, some hints point to her either being Wolverine’s daughter or a creation of the Phoenix Force, with there being no biological father at all.
In the reality shown in What If (1st series) #27, Phoenix was not the last X-Man to remain standing in the battle with the Imperial Guard over her fate. As such, she did not turn back into Phoenix. The X-Men having lost the duel, there was nothing they could to stop the Shi’ar performing a partial lobotomy on Jean, with the intent to block the access to her powers forever. Now simply human, Jean stayed with the X-Men as mansion staff. Eventually, though, the Shi’ar asked the X-Men for help when one of their planets was attacked by Galactus. Jean accompanied the X-Men but, seeing them being defeated one by one, she re-manifested her Phoenix level powers and single-handedly convinced Galactus to leave the planet unharmed. In the eyes of the Shi’ar, she had redeemed herself and, as such, was allowed to rejoin the X-Men full time. For a while everything was fine, until Phoenix’ hunger returned. At night, she would sneak out of the mansion and soar through space to devour asteroids and even a small star with no inhabited planets. When the X-Men discovered this and called on her behavior, Phoenix angrily lashed out and killed her teammates one by one. The shock of seeing her lover, Cyclops, dead caused her to destroy everything around her - starting with Earth itself and not stopping before the entire universe went down in flames.
Another timeline’s Phoenix, depicted in What If (2nd series) #32-33, too was lobotomized by the Shi’ar. Shortly afterwards, Magneto approached her with the offer to restore her abilities, but she rejected him. Instead, she married Scott and lived quite happy for a while. They even had a daughter, who they named Rachel. One night, Mastermind snuck into the mansion and took revenge on the now powerless Phoenix. After he shot her multiple times, she remembered who she truly was, not Jean Grey, but a cosmic Force who took on her shape. She visited the cocoon at the bottom of Jamaica Bay and, fearing that Scott would no longer love her if he knew the truth, she atomized the real Jean Grey only to resume her life. However, she was living a lie for the next years, pretending to have no powers, while secretly helping out the X-Men or mutants in general every once in a while. Eventually, her actions were discovered and after consulting the precog Destiny and learning that in every future she would cause much death and destruction if she remained on Earth, she left husband and daughter behind and returned to the stars.
What If (2nd series) #37 shows a reality in which Wolverine became Lord of the Vampires. His bite transformed many of his fellow superheroes into vampires as well, among them the members of X-Factor, including Jean Grey. During Inferno, Jean had to battle Madelyne Pryor. At first, the mutant vampire and her demonically influenced clone seemed evenly matched, but Jean gained the upper hand when she accepted the Phoenix Force back into herself. She then used her awesome might to disintegrate Madelyne and her ally, Dormammu. Yet another notable difference regarding this version of Jean is that she is her timeline’s nexus being, just like the Scarlet Witch is the one for the main reality.
In the Age of Apocalypse, Jean was one of Magneto’s X-Men until she was captured and imprisoned by Sinister. Logan, aka Weapon X, finally broke her out against Magneto’s orders and both of them left the X-Men after that, becoming lovers. When Weapon X aided the European high council who intended to nuke the Apocalypse controlled North American continent, Jean left Weapon X and returned to America in a last ditch attempt to stop the bombs. She teamed up with prelate Summers, aka Cyclops, and learned that she was the mother of Nate Grey (whom Sinister had created from DNA stolen from both Jean and Cyclops). When the bombs rained down, Jean was shot by Havok, though she still managed to stop the bombs from detonating. For a long time, the world believed that Magneto had saved them, as he had allowed Mr. Sinister to take the unconscious Jean’s body. Eventually, though, the truth came out and Jean, now wielding the Phoenix Force, became the new leader of the X-Men.
The Jean Grey of the alternate Earth X future had apparently lost her powers at some point - a blessing in disguise as all active telepaths were killed by the Red Skull. A middle-aged, dumpy woman, Jean led a rather unhappy life with Wolverine. At one point, she walked out on him by announcing that she was really Madelyne Pryor, though later on she explained to have only said that to spite him. Still, a shadow of doubt regarding her true identity remained.
This Jean had been replaced by the Phoenix Force for a while too and, having been loved by her, Cyclops could not go back to being with the real Jean, finding that relationship lacking in comparison. Their psychic bond remained intact even after Phoenix’ death, and the lovers continued to communicate with each other
across the border that separates the physical realm from the afterlife. When the heroes gathered by the Kree warrior Mar-Vell succeeded in defeating Death itself and created a new paradise for the dead souls to ascend to, Phoenix became one of the seven Guardians of the Paradise.
Jean’s history in the Mutant X universe is quite muddled. Under the name of Ariel, she was a founding member of the X-Men and in love with their leader, Havok. Later on, during a time that Jean was believed dead, Havok married her look-a-like, Madelyne Pryor, obviously Jean’s clone. When she re-surfaced, Jean was working together with Sinister and Apocalypse to recruit the aid of Havok’s new team, the Six, against an evil Xavier. That crisis having passed, Jean joined the Six, as Madelyne had been turned into the Goblin Queen and was no longer with them. Jean also mentioned having been in a relationship with Wolverine, and to having worked with SHIELD for a while, though it was unclear where exactly these events fit in with her history.
Another counterpart of Jean Grey had most of her powers taken away for crimes unknown. Banished from her own universe, she ended up on Earth 998, where she pretended to be a reincarnation of the recently deceased Queen Madelyne. The evil Jean set out to become not only queen of Britain but of the entire world. To reach that goal and find a way of restoring her powers, Jean looked for the ultimate weapon across the multiverse: Nate Greys. She lured quite many of them to her kingdom, though most of them died after having been used by her for a while. Queen Jean also traveled to the main universe where she replaced Nate Grey’s companion, Madelyne Pryor, wormed her way into Nate’s mind, and returned to her world with him as her weapon. However, Nate eventually broke free and killed the evil Queen Jean before she could do any more harm.
In the Ultimate universe, Jean is a young woman in her late teens. Originally plagued by visions and driven insane by her immense psychic powers she was found by Professor Xavier in a mental ward and he trained her to control her talents. As Marvel Girl, she and Cyclops recruited the newer X-Men. Jean had a short-lived affair with fellow X-Man Wolverine before settling with longtime crush Cyclops, who gave her some stability. Recently, her visions of the Phoenix returned and the Hellfire Club tried to turn her into a vessel for the Phoenix god. Jean became incredibly powerful and manifested a different personality; though it is unclear whether Jean was possessed or created that new personality herself. Jean believed the latter and seemingly regained control again. She has, however, manifested a Phoenix raptor several times since, as well as a lack of self-control such as when the X-Men were attacked by mutant haters and Jean killed them.
A time-traveling experiment gone wrong created another divergent timeline, one in which present day heroes emerged in the 17th century, the year 1602 to be precise. Mutants were referred to as “witchbreed” and, as such, were feared and hunted. In this world, Jean pretended to be a boy ”John Grey” to be able to attend Carlos Javier’s school. Javier and all of her teammates save for the newest member, Angel, were aware of that ruse. Potentially the most powerful of Xavier’s students, she exhausted herself when she had to carry a ship a long distance and perished, her last wish to die as a woman. At her funeral pyre, Angel believed to see a bird shaped image emerge from the flames. Whether that had a future meaning, nobody can tell.
In a reality where [What If ...] Magneto and Professor X had formed the X-Men together, Xavier did not return to the United States and as such was not around to help a young Jean Grey. As a result, she remained in her catatonic, comatose state for nearly 20 years before she aroused the attention of the two X-Men founders. Probing and examining her, Magneto noticed several oddities and was not sure whether it was safe to wake her up. However, when their school was attacked by mutant-hunting Sentinels soon thereafter, Jean woke up and, wielding the Phoenix Force, she saved Xavier’s life and defeated the giant robots all on her own. In the aftermath of that incident, she joined the team.
Ten to fifteen years in the future, the re-appearance of Phoenix heralded the End of the X-Men. Though it occurred in deep space, the ramifications of Jean’s rebirth were felt on Earth by her friends and family. As a series of attacks on the X-Men originated in Shi’ar space, Phoenix met with her teammates on Chandilar, only to find that Cassandra Nova was the Mastermind behind them. Against all odds, Cassandra managed to beat Jean and wrest control over the Phoenix Force from her. However, Madelyne Prior, who had accompanied the X-Men in disguise, turned the tides upon realizing who she truly was - - the part of Jean Grey that always loved Scott more than life. With that realization, the two women - Phoenix and Madelyne - became one, as Maddie uses her last strength to heal the mortally injured Phoenix and Scott. Madelyne/Phoenix, along with several other X-Men, then recreated the “Tree of Life” from the Quabala and presumably transcended this plane of existence.