In pertinence to stunning aliens...

[cylonspy]

So, I'm kinda a newb, but I stunned the last alien in a mission (in 2.5) with a stun rod,  but nothing happened. The alien was successfully stunned, but the mission didn't end, and I searched the entire map searching for any remaining aliens. I wanted to check here if there was something I missed.

[DarkRain]

No, that should be it, if you are sure you didn't miss any alien then the mission should have successfully completed when you stunned the last alien.

If you still have the log from that session (ufoconsole.log) you can attach it here so we can have a look (keep in mind that the log is overwritten every time you start the game)

[cylonspy]

I'll try and see if I can replicate it again, then. Thank you.

[TBeholder]

The most likely reason is that the last alien failed morale check - in which case it dropped weapon, ran away, hid in some corner and cowered in fear there.
Did you see any dropped weapons not accompanied by an alien corpse?

[cylonspy]

I already ruled that option out. It kept crashing when I attempted to replicate it (which is an already posted bug), so I'm currently going through the 'absolute joy' of attempting to compile the latest version into a useable app bundle for my mac.

Yaaaaaaaaaaay