This sounds like an interesting take, as well as a potentially more logical role for a clandestine organisation in an an alien invasion. (or at least in an alien invasion that can possibly be defeated).
If in X2 the xenonauts are a small group of humans occupying a military facility, filled with alien tech and striking stealthily at targets all over the globe, including non alien controlled government facilities, then how do we know that we aren't in fact a mind controlled alien infiltration cell? Or the player is in fact an alien, convincing a bunch of poor humans they're actually opposing the invasion... "No no team, don't dump the alien corpse in public to bring the infiltration into the light, that would cause... errr... panic! Yes panic is much worse than all levels of government being stealthily infiltrated to eradicate humanity."
On another note, if the team is going to be attacking government bases, then there are three ways to present themselves:
1. As Xenonauts: They may have a hard time believing you are stealing guns and killing troops for the good of humanity. you look like terrorists to the government, so they will try and wipe you out.
2. As a foreign power: This looks like a normal attack, so they won't be looking for terrorists but they will be massively upset by this action by a foreign power. This is absolutely terrible, as if the aliens are trying to spark a nuclear war, then you're doing their job for them (and probably even better).
3. Impersonate aliens: You get to grab the loot and make the world more suspicious of alien activity. Maybe leave an alien corpe so the soldiers think they killed it to really sell the ruse. This way you don't get the heat and the aliens do, which is great, but if you could pull it off why not instead just publicise the proof of alien invasion and get all 4.5 billion 1977 humans mobilised to stop them?
There is an interesting dynamic, where you have three sets of factions: governments, alien infiltration cells and xenonauts (are you the only vigilante group out there?).
Aliens want to increase government - government tensions to spark nuclear war.
Xenonauts want to increase government - alien tension to get a mobilisation to stop the infiltration.
Then the xenonauts can't necessarily tell the difference between an alien cell and another group of xenonaut terrorists... I mean "freedom fighters". So they want to stop alien infiltration cells from raiding bases etc while not wiping out potentially friendly vigilante groups using alien tech to fight aliens (and also themselves attacking government bases because they need more stuff to stop the aliens doing just that?!?).
I think there is the basis there for quite an interesting infiltration strategic dynamic, but that could be a ways away from the intended gameplay.
One of the big strategic things that needs to be rationalized is why they don't just go public with the aliens. it could be that this is a mechanic, and you have a choice with loot and corpses or captures: research them yourselves to increase capabilities, or pop them off to be dropped in a public place to convince people that aliens are here (and somehow it takes several sectoids in times square before the sheeple wake up!).
