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Had various side-lines off of our long term game:
Group of scientists on a unexplored planet watching over a transported colony of aliens.
Orion pirates - hee, hee, hee
A few "short stories" set on a few different colonies, colony-federation interactions mostly.
A brief, but interesting, "talamasca in space" -style attempt to bring a supernatural bent to trek. Didn't work real well but could get interesting IMHO. A lot of the exotic aliens Kirk et al run into could be followed up on by such an organization...
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Ran a couple of campaigns with all rogue (but good-hearted) rogue groups:
1) A flipside of the "Think Tank" from Voyager. Scientist and engineer PCs who roamed the AQ in their own ship helping people solve problems (and who Starfleet couldn't help due to the Prime Directive).
2) "Noble renegades" campaign with a bunch of people of dubious employment (smuggler, bounty hunter, former netgirl, ex-assassin) on the run from the authorities and former associates who wanted them dead, occasionally helping those in need. The group "leader" was the ex-assassin, who was half-Romulan and had worked for the Tal Shiar before he finally woke up to the fact that his victims weren't always "enemies of the state".
3) Traders (and part-time smugglers) in a jazzed-up freighter who got whisked Voyager-style far from the Federation (around 30,000 light-years) by a subspace anomaly and now have to get home. But without Starfleet regs and the Prime Directive the moral issues won't be quite so clear-cut...