What do you think, would an EndWar/X-Com cross work?
Like, the invasion begins during WW3. Instead of an international effort, the US and the Europeans both make their own military groups for responding to the alien incursion. These groups initially don't know about each other until they run into each other in the middle of a terror mission. Joint asskicking ensues, after which they agree on never having seen each other; their respective countries are at war, after all, and admitting that they collaborated with enemy combatants could get everyone court-martialed.
It later turns out that Russia also have their own anti-alien team, except their agenda doesn't align with those of the others. In keeping with their portrayal in EndWar, they intend to just sit back and defend until the other sides annihilate each other, then swoop in and be the laughing third. They're not outright collaborating with the aliens, they just want to exploit the situation to their advantage.
Things get complicated further when WW3 starts to drag out and the US and European teams face the possibility of what tech they gained from the aliens being used not to fight the aliens, but their nation's human enemies. Naturally, they do not agree with that, as escalating a world war by arming their nation is not what they signed up for.
An interesting idea.
Is this set before End War?
During EndWar.
Ah...
Hm. I got Fanfic Fuel ideas that may do crossover between mediums. But that'll have to wait as I need to sleep soon. 
Also contemplated the possibility of a Code Geass / Red Alert 2 crossover where Lelouch commands his troops using EndWar's Overlord interface. Like, he sits inside a command truck on the edge of the battlefield with a VR helmet on his head. At least, I think that's how Overlord would work in-universe.
But then again, that's not really an idea that belongs in this thread...
Really thought on an idea based on the Rainbow Six series, but with Patlabor's 2nd movie (So far) with a mixture of the two OVA episodes, where the movie got the inspiration from.
Hereford gets called in by Tokyo to be covertly deployed after the Japanese Defense Agency gets rumors that some of Tsuge's supporters are in Tokyo, awaiting word to create a coup-like atmosphere.
Rainbow sends a team in and then they help out SV2 take down Tsuge himself.
With "The Division" coming out next year, it's basically potential Fanfic Fuel for whatever's happening in the US.
Including the islands governed by the US. Will they be independent? In chaos?
https://www.fanfiction.net/game/Division/
The Division has eight stories written.
Seeing the Blacklist and how it worked out, I was thinking a crossover with the Full Metal Panic! franchise.
Dedicating this thread to the memory of Tom Clancy, one of the best thriller novel writers who wrote Rainbow Six and the Patriot for starters.
Anyway, this is for novels/games done by him or by Redstorm (now part of Ubisoft) with stuff ranging from the novels done by him like the Ryanverse, Op-Center, Net Force and games from the Ghost Recon and Splinter Cell series.