I noted somewhere (this forum ?) someone else having this problem.

My squad stuns a lobsterman commander at a colony, returns to exit with specimen, and ends mission. The squad is credited with a live alien. However, the specimen is not onboard when the ship returns to its home base. (though, once it did but disappeared enroute to the research base).

I have had the specimen in a backpack, have carried it in hand, and have left it on the exit floor. Same result in each case. What gives ?

I have this fear the answer will be to upgrade to V. 2. Having invested much time in this game, I hope there is another answer.

It would be in your best interest to update with the v2 patch - but it doesn't hurt to attempt to finish your current game beforehand.

I think the containment modules can get a little buggy. My advice would be to clear up as many live interrogations that you can before you attempt another capture of a commander.

If things really aren't going well, you can try and empty your containment completely with a bit of file copying trickery. Save a brand new game in a new save slot. Then, copy the file astore.dat from the new savegame to your old savegame. This should wipe out everything that's currently in containment. I don't think it'll affect any interrogations in progress.

- NKF

Shouldn't do. You only need artefacts in stock to start research programs; not to finish them.

Thanks for your comments. I tried the over write of that file, but that didn't work either (aside from allowing the commanders showing up dead).

I'll just have to start over. Captremf