I got two ideas, 1. we have crossovers, like with the Romulan Hobus mission and the Starfleet Iconia mission where its the Rom player that scrams through the gateway when Starfleet shows up to apprehend Taris.
2. A few more missions where you have the player beam an away team, but just stay above the place and defend like the system patrol with the NPC ship Da Vinci.
Some more ideas are a feature breather episode about daily work, observing a less advanced world or some cosmozoan, repairing a damaged ship/base, or cleaning up after the Enterprise or its KDF equivalent.
Also, a minor task on Risa based on the players career might be nice (tac sci eng)