What about having our captains (or ships in their entirety) abducted by the temporal police of the 29th century? They have need of our captain or ship for some mission in our time frame. A bomb has been planted at a star base or an ex-federation personnel has escaped into our time frame and we're needed to get them back, as we knew their ancestors or something of the sort. Some type of mission (or preferably series of missions) where we're needed to time jump to past (or future) star bases, planets, or another federation vessel. Maybe we get stuck in the 1800s on earth? Or maybe the 20th century as Captain Janeway did in one episode. Some kind of time travel and interaction with the temporal police would definitely make interesting missions in my opinion.