Raven and her lover/wife, Irene Alder, raised their adoptive daughter Anna-Marie until she and Irene tested X-Gene positive and were arrested, while Anna-Marie was not tested and evaded capture. She was paraded among other captured mutants in the streets by mutant haters.
She eventually escaped or was liberated by unknown means, although she was believed to have died in custody. It remains unclear as to what happened to her life-partner, except that she was stated to have died as well.
Later Mystique came into contact with Magneto and seems to have worked with him for some time. She was present when Magneto used New York City skyscrapers to create Fortress X, a safe haven for mutantkind.
Mystique began caring for the children of Fortress X. When the Human strike force, The Avengers, invaded Fortress X, Mystique was killed by Captain America while trying to protect the children. Her last words to Captain America, and realizing the brutality of what he had done, prompted him and the Avengers to abandon their mission and lay down their lives to save Fortress X from the Hulk.