Just one more AU. Specifically, it's from an early 90s two-parter in
What If? vol. 2 #32 and
#33. George Caragonne wrote it based on some plot ideas by Claremont.
In the timeline of these stories, Jean was replaced by the Phoenix just as she was in 616. Then, similar to Claremont's original ending of the Dark Phoenix Saga, Phoenix-as-Jean had her powers deactivated by the Shi'ar and married Scott. Together, they had Rachel. Eventually, Phoenix-as-Jean got her powers back, found the real Jean where she left her in the stasis pod at the bottom of Jamaica Bay, and, in a moment of weakness, wished the real Jean out of existence.
In Rachel's timeline, meanwhile, the Phoenix bonded with Jean instead of replacing her. Scott and Jean got married and had Rachel. Jean was subsequently killed when Mastermind detonated a nuclear bomb in Pittsburgh. Scott raised Rachel until he was killed at some point during the Sentinel takeover.