Oh. If you want a REALLY nasty villain.
Should you be playing Starfleet then at the very last have him surrender into their custody. As Starfleet officers they SHOULD now be bound to by law into taking him in and not sumerily executing them.
Once safetly in the JAG have the villain either;
A-Cut a deal, offer up a bigger fish in exchange for his freedom (in which case he can easily come back to haunt the players later)
or B... Reveal his collected evidence (real or fabricated) that casts suspicion over the players themselves. They thought chasing their nemesis around the galaxy was hard wait iuntil they have to defend their actions in a court-room.
(oh, and if they DO execute their nemesis, then you still get a courts martial...)
By the end of the court session, if they clear their names, they can now all be assigned a new enemy of the JAG officer who they just soundly beat...
Sometimes your original nemesis may have revenge tactics beyond the whole 'blowing stuff up' line of work and will happily settle for career destructilon...
DanG/Darth Gurden
The Voice of Reason and Sith Lord
“Putting the FUNK! back into Dysfunctional!”
Coming soon. The USS Ganymede NCC-80107
"Ad astrae per scientia" (To the stars through knowledge)