How to bring them back?
One: The original team gets back from dealing with the Plodex and is shocked to find that they've been "killed". They set out to "set things right".
or
Two: The originals were "killed" by the Collective, but are swept up by Dept. H and kept "on ice" with Chuck Moss being forced to "hold their souls" (like Michael did in X-Men Unlimited). Eventually someone, Logan or Walt, find out about them and breaks everyone out. Wanted by the government, AF must defend their country while avoiding re-capture or worse.