Origionally posted to the old forum by [Shran]
I’m currently running a campaign where no one is serving in Starfleet. Although it didn’t quite start that way. I just wanna share summaries of some highlights which may give you some ideas for your own adventures.
THE GATHERING
First adventure: The main characters are Starfleet officers and they discover an android, who is the only non-Starfleet character. A new coalition is forming from minor powers in the alpha and beta quadrant: Tzenkethi, Gorn, Kzinti, Talarians. They oppose the Federation because they are the ones who also suffer when the Federation once again meets a super powerful enemy who wants to destroy it (Borg, Dominion, etc.) The adventure was basically introducing the characters and hunting down a vital energy source for the android (who actually consists of parts that came from the future).
SHADOW OVER BENZAR
Another adventure was about Benzar. During the Dominion War, the Romulans retook Benzar and now the Federation is trying to negotiate with the Romulans so they give it back. The crew’s ship was on its way to Benzar and was ambushed by Romulan Warbirds. The ship was destroyed and all PCs were dead. As a GM, I tried to blame myself for bad balancing and suggested to just restart the adventure. But the second time I made some of the crew have flashbacks. Turns out they were in sort of a time loop, only it got easier each time. The crew was actually on a Romulan Holodeck, with the Romulans trying to gather intel on what would happen if they just kept Benzar with military force. Later in the adventure, the crew discovered that they were actually holograms themselves and the were on a Warbird-turned-holodeck that continuously lost power. This made for a great finish as the PCs were randomly deactivated until only one was left sitting on the captain’s chair. So not connected to the campaign but nice standalone and it worked well fooling the crew the first time so that the players didn’t discover the time loop too soon 
EXODUS
There is political unrest in the Federation. Sauria has elected a new chieftain who unexpectedly won the election. This is a great shock because the first political act was to declare that Sauria is seceding from the Federation. This has Starfleet in panic because they don’t really know how to deal with it and also suspect outside influence. So they begin blockading the planet. Meanwhile the crew is on the planet speaking with the political opposition. A mob storms the party’s HQ. In the mob, the crew spots non-Saurians with guns and tries to take them out by shooting them, which does not really defuse the situation. Later they find out that a secret Starfleet test lab has been raided and explosives have been stolen. Starfleet thinks that the explosives are smuggled from the planet by a civilian transporter, masking the explosives with normal life signs, however the crew is unconvinced. They discover an alien on the planet who can read their minds and control the android. So the android PC was basically the end boss 
Back on the ship, Starfleet orders the crew to shoot down the civilian transport but the PC captain refuses because he thinks it is just a ruse.
In the end, all PCs are kicked out of Starfleet. Two for shooting into an unarmed mob (the video recordings conveniently don’t show the armed inciters) and the captain for refusing orders.
MIRROR OF SOULS
So now the crew is out of Starfleet and without a ship. I let the players decide their next ship and they picked a Defiant class. So a transporter accident got them to the mirror universe where they stole a damaged Defiant class from the new Terran Empire. From a previous adventure, the android remembered four important planets which the crew now has to visit.