It's all about timing.
If I were running the game (which I couldn't do, I could never find the time, especially not now!), I'd start things off with some occasion for a lot of reunions, various X-Men coming back from this, that, and the other, perhaps after some period while there had been remodelling after a fight that did some serious damage to the HQ (whether this will be Westchester or Snow Valley doesn't really matter for this purpose). So two characters who hadn't seen one another in a while could suddenly fall into bed, or sit and talk about what they'd been doing while they've been apart before fucking like crazed ferrets, or deliver Ominious News and discuss it gloomily for a while before getting eaten out and fucked -- just to cheer things up, you know.
Once the opening sex scenes have started to wrap up, somebody starts sending messages via intercom or telepathy, breaking in just after the cuddly afterglow is about to get old for each couple or troika or what have you, each in turn. That summons everybody to a meeting which amounts to a Council of Elrond, where Emma or even Charles dispenses Massive Exposition, and the inital version of the problem as our heroes best understand it so early on in the plot. This leader then sends one group after another off on various missions, or even the whole kit and kaboodle off to a frontal attack on some enemy who won't be prepared for them; if the latter, an initial assault would naturally break down as clusters of characters break off on their own from other clusters.
Once the scenes splinter things like rape scenes can happen without so many allies being close at hand that rescue is inevitable, and heroes and villains can duel, even kill one another. Where things go from here would depend upon how many players are still involved, and an organic development of the plot which should be able to branch and grow on its own by now, arising from chemistry between characters and writers, and from the logical consequences of how a scene finishes up (the henchman escapes with the McGuffin, the captive guard is interrogated/seduced/bought off and reveals what he knows about the mastermind's evil plan, etc.). You get the idea.
What do people think of this?
The viral idea is a good one, but it reminds me a lot of Love Mansion. That's not a good enough reason not to employ it, of course; but unless we want to considerably expand the opening scenes, it wouldn't fit here, unless it's just a short-term sex gas thing set off by one of the heroes on purpose as a prank or somesuch. If the virus is to be used here, I think that it should be the main theme of the first part of the game, instead of the scenario I described above.