Wanna run this with comrades. By default I run everything in Genesys and I think it would handle this well, but I'm curious if there's something that would be more lightweight and setting specific for it.
If you want it to be narratively driven there's certainly a PBTA strain out there for this. Otherwise this fits the bill for Delta Green almost perfectly. Stars Without Number if you file off the spaceships could do it reasonably well.