Timeline A: 2006

Jean gets “better,” by which we mean “is resurrected by the cosmic entity known as the Phoenix.” The X-Men and Magneto’s brotherhood, fighting over a purported cure for the X-Gene, decide to put aside their differences to stop Phoenix from destroying the entire world. Phoenix kills Xavier (who actually gets better shortly after), Wolverine kills Phoenix, and relative peace comes to mutantkind, granted recognition and rights for their acts saving the world. (X-Men: The Last Stand)