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This sounds like something that would be a great rpg run.  Have you been able to play test?  How did it work?

While I fully understand wanting to drive a narrative, but requiring the players to play two specific armies you are setting up limits that might make players gloss over your mission, thinking "I don't have any aliens" and so not give it another look.  Is it possible to play with other factions?  If so, state that in the rules and the recommend the two factions you'd prefer, rather than make it prohibitive.

While both have "different" objectives, they still have to do both, and will have to work together.  There doesn't feel as strong a sense of competing objectives, or shifting objectives, as the Jam theme suggests.  They both do the same thing, the only decision is together or apart for most of it.