We're told that the Changeling approached Xavier. He had a terminal illness and wanted to make a difference for good in his final six months. Xavier told him to take his place, telling only Jean, and giving both Changeling and Jean some of his mental powers (explaining why the fake Xavier was able to mindread).
This seems a fairly horrible thing to have done, but well in character for Xavier. Nobody calls him on it, but I guess they're used to him by now. It makes a particular nonsense of X-Men #46, which has the Juggernaut accidentally released due to lack of maintenance of some science kit. Why has he done this? He found out about the Z'Nox coming, and has been plotting all this time. His plan involves the X-Men being present, which also means the business of them being forced to split up by the FBI in #46 was an unexpected risk factor.
He decides not alert to the Fantastic Four or Avengers. Or SHIELD. His plan is disrupted slightly when Nick Fury and the helicarrier are there to meet the aliens at the south magnetic pole. They - including Alex on his first official mission (rather than just being caught up in events) - proceed immediately back to Antarctica in a rocket. When they are in place, Xavier uses his immense mental powers, in combination with Jean and Alex and Scott, to project feelings of sympathy and mercy (Bobby is tapped to provide cooling for this arrangement). This works out quite well, and the Z'Nox withdraw. Xavier has been severely strained by the encounter, and we are left with the question as to whether he'll survive. (!)