Hey just recently joined the forum here, and sorry this is such a late reply to your question, but perhaps it can also help others who recently joined and are looking for the answer. It has been posted somewhere else in the forum, but here is the solution once again...
As you see the station being destroyed, stop your ship and watch,
don't get any closer. As the station (and Ray in your old ship) are destroyed, retreat to the nearby portal. This is meant to happen, and "Ray's" ship is now your new Mothership. You should shortly get a new Mission objective to return back to Placid Docks and see your old friend Alex again.
