I would have had them get home in the first two minutes instead of the end. A group of Starfleet security officers beams aboard and immediately arrests Chakotay, Belanna and the other Maquis and ships them off to prison for their time as Maquis. Just because the crew had to forgive and forget in order to survive doesn't mean Starfleet is going to. They also send Paris back to prison to finish his term there. The Doctor is taken out of sickbay and sent to a lab somewhere so the scientists can see the effects of his program having been on so long. Seven is also arrested, but sent to a lab to be dissected so Starfleet can learn how to beat the Borg once and for all. Janeway, Tuvok and Kim spent the episode trying to get their friends out of trouble. In the end, they get their friends off, Janeway reassembles the crew on the Voyager and they fly off to have normal Star Trek type adventures.
The End
As dark and sad RandyS 's scenario is, it is certainly realistic.

Indeed, we must not forget that it is not because Janeway and her crew have become accustomed to see Chakotay and his Maquis crew, the Doctor and Seven as friends that the situation had to be imposed on Starfleet/the Federation. That's why I truly think that the "after-Endgame" could not necessarily mean a happy end for everyone (after the Voyager's reunion party, of course!


As for Harry Kim, I don't know why but I don't see him live (and prosper) a longtime in Starfleet institution!
No doubt he has many qualities (smart, kind, courageous, for ex.) to become a perfect gentleman for any women (even if until now, his experiences women and capable man and a brilliant officer but he is very ambitious too and to quickly advance to more senior roles, he would easily embark on challenges, without
without weighing all the consequences. => or he would be killed in a mission or he would resign further to a mission which would gone wrong because of an error of assessment/miscalculation from his part, causing many casualties.
Indeed, he will not always have a Janeway, Paris, Torres or Seven with him for reason him, when the situation will be complicated!
