[Humabout]

Originally Posted by Major_Eclectic

(a) anyone has any suggestions about how I could take that basic concept and make it a fun adventure

The overall structure I'd suggest is this:
1. Receive orders to investigate the mission ship.
2. Fly out, find wreckage/derelict/whatever is left. Allow initial investigation with some minor clues (maybe a What clue related to the nanobots)
3. Get distress call from another ship currently under attack in the area. Mention something related to a clue the PCs already discovered to entice them to check out the distress call.
4. Either (a) the second ship is already done for, but more clues are available or (b) the Odyssey's arrival chases off the alien ship and the PCs can get clues directly from the ship's crew. They can also calculate the alien ship's course from the attacks and/or escape vector.
5. Confrontation! The ship catches up to the alien vessel. Give them a reason to board it, so they can discover the stasis stuff and visit Moralityland.
6. Conclusion! Whatever the heck they decide to do and live with it.

Don't forget to have them make deduction rolls along the way and give them access to records in case they want to see if there's a pattern to the attacks. This sort of legwork on the PCs' part should let them skip some of the scenes above as a reward for creative thinking and possibly making their own scenes.

Originally Posted by Major_Eclectic

(b) if anyone else can think up some other cool Star Trek-esque space adventures for the Confederation Starship Odyssey?

There's always the classic First Contact situation and everything that can go wrong. Especially if the crew wanders into the middle of some sort of dispute between two previously unknown species!

A frontier merchant requests help because a frontier alien warship attacked him and he barely escaped. Investigation reveals that the merchant stole something from the aliens and they want it back. Maybe make the merchant a quirky and likable con artist who can't seem to help himself.

Um, honestly, you can probably rip off and reskin most of the TOS Star Trek episodes. For variety, look at all of the Star Trek knockoffs, too - Babylon Five (early seasons), Dark Matter, Lexx, Farscape, and Firefly off the top of my head, and I know I'm missing a lot.