I'll bump you up to full marks for Theme because if it's there and I'm just not familiar with the specific myth, that's not on you.
Regarding clichés, there are basically two Mothership plotlines you'll see over and over for dungeon-crawl type formats. "Science Experiment Went Wrong," and "Mysterious Alien Device Turned Out to Be Bad." And in the science experiment version, there is usually crew (or in this case animals) that got turned into monsters, and it's almost always the scientist who's the BBEG, often in disguise when you first meet them.
Take a look at Project Indigo in this jam and you'll see what I mean... although the map is much smaller, the storyline for this one and that one are structurally almost identical.
For sandbox formats, there is a third cliché, which I guess you could call "Soylent Green is People!" where you're wandering around offices or a factory until you realize that what they're doing is even more horrible than you first thought.
To be fair, I think part of the issue here is with Mothership itself... it's a game that lends itself heavily to these structures.