[Duran Man]

Here's what I quickly came up with:

Phoenix didn't kill Scott. Instead, she sent him to the Axis of Time from where he tries to contact Professor X, and the remaining members of the X-Men in the apocalyptic future. Scott tells the professor that an assassination by the Brotherhood in the 60s is what triggered all of the events leading to this future. Xavier is able to send Scott back to the 60s to meet the original members of the X-Men to help change the future.