I tossed an idea out somewhere on here about a war between the cannon established MU, and the one that appears in some books, where the Empire didn't fall, but continues into NG era. In order to get your characters involved, maybe this fight is spilling over into the 'regular' SF universe, and you can either try and stop the war (or at least incurrsions into their universe), or join one side and blow up the other one!
I had another idea, influenced by both Marvel's orginal "Secret War" (where good and evil superhumans were gathered by a cosmic entity to see which is better), and the TOS episode where the Excalibans did the same thing. In it, some force gathers characters from various eras, timelines and maybe even universes. They are united against some uber-threat that threatens (as they are want to do) the whole of reality. Or, go bigger scale, having not just persons, but ships.
I thought it would be fun for, say and ENT era captain to see where Earth stands in the future, or a DS-9 era captain to see Vorta, Borg or even Founders as SF officers!
_________________
"Yes, it's the Apocalypse alright. I always thought I'd have a hand in it"
Professor Farnsworth