Mission 8, the Skedar Assault Ship in the first game has enough enemies thrown at you to definitely be That One Level, but realistically speaking, it is surprisingly undermanned for such a massive vessel. There are large rooms that only have one or two warriors in them when they could fit far more. However, if you visit an optional location in the ship to obtain a Slayer rocket launcher, you pass by a large stasis chamber with a large number of Skedar in them. Apparently the majority of the crew is in cold sleep. It is also mentioned in the briefing files that the war with the Maians has been taxing on the Skedar as a whole, so the ship is probably running on a skeleton crew even with the warriors in stasis.
Fridge Horror
Since the Skedar captured Joanna and Cassandra and brought them specifically to their home planet instead of just killing them on sight, what exactly were they planning on doing to them? Torture? Public execution in some horrific way? Who knows?
Given the Skedar's track record in their Religion of Evil, an horrific sacrifice seems most likely, though how they plan to murder them is never revealed.
It can be safely assumed that dataDyne beat and tortured Mr. Carrington extensively, since they had him tied to a chair in his basement, and got him to give up the location of Dr. Caroll. They probably didn't just ask nicely.
Consider how many enemies you killed on each level throughout the game. How many of those weren't bad people at all but just US military personnel trying to protect government property from foreign spies? (dataDyne is different though since they're pretty much Blackwater/Xe/insert choice of unethical megacorporation here.)
Who knows what kind of unethical human experimentation went on at Area 51 before Joanna got there? Chemical brainwashing, toxic nerve gas and alien vivisection are just the tip of the iceberg. These guys probably got up to all kinds of Unit 731-worthy stuff.
