History
The past history of Madelyne Pryor mirrors that of her Earth-616 counterpart. When X-51 looked into the past to see what many of the surviving X-Men done in the passing years, he learned that the X-Man eventually became the mutant terrorist known as Stryfe and died protecting a woman who he thought was Madelyne Pryor. If this was indeed the true Madelyne Pryor or not remains to be revealed. On Earth-616, Nate Grey was manipulated by the Jean Grey of Earth-9575, who posed as Madelyne Pryor. Since Earth-9997 is a divergent reality from Earth-616, then it's likely that this version of Madelyne may be from an alternate reality as well, however the truth remains unrevealed.
In modern times Wolverine and Jean Grey would start a relationship and live together and eventually devolve into the stereotypical bickering couple. Disgusted by Wolverine's lack of action when Captain America's forces where battling the Skull's army in New York, she would leave him. Before going she would tell him that she wasn't Jean, but Madelyne Pryor[1].
However, during the wedding of King Britain and Medusa, Jean would be in attendance with many other surviving members of the X-Men. She would admit to Wolverine that she was lying about being Madelyne, and only said so to "snikt" him[2].