It appears I have killed all of the aliens, yet the mission will not end. I debugged and revealed everything. Nothing is alive. I did not see any errors, though that doesn't mean there weren't any.
save_Mothership No Finish.zip
oh damn was sleep ( missed stream
No worries! Sleep is important.
How was the last enemy incapacitated?
It seems that Battle::checkMissionEnd() hasn't been called, which should be checked every time a unit is downed or retreated (and indeed, retreating one of your own agents calls it, where it recognizes there's no enemies left and starts the mission-end timeout)
Hmmm...I don't recall. I would have to watch the video. I would imagine the last enemy was killed by toxin c. I ended up completing it via the quit or exit mission option.