Harking back to the inital run, the X-Men suddenly remember that the government has a lot of computer information on them. That Robert Kelly is on the telly - on Panorama, in fact - scaremongering about them (the interviewer's name is Mr. Cheever. In a strange coincidence, the only famous Cheever died in the cover month). And the X-Men have suddenly somehow become "outlaws" (that happened as early as #154, according to a caption there - before the property damage of the Shi'ar arc). They decide to infiltrate the Pentagon, and introduce a computer virus to erase what exists. A caption repeats the urban myth that the Pentagon was originally designed as a hospital.
So, Colonel Carol Danvers (who's found that some of her advanced physiology as Ms. Marvel is still present), Captain ??? (I wonder what name Logan was using on his ID here - there's no reason at this point to suspect that it isn't something like John Logan or Logan Smith), and their civilian colleague Ororo, bluff their way through the security at probably the world's most heavily guarded government installation. Making their way to the target, they embarrassingly bump into Mystique and Rogue, of the Brotherhood of Evil Mutants, who are also infiltrating the Pentagon. Mystique is using a cover identity of "Raven Darkhölme", which is surely not her real name, and she shifts back to the blue-with-white-clothes form when she's knocked unconscious, which is a bit unfortunate. Rogue has got her canonical set of power-stealing powers, on contact with flesh, and has recently acquired the powers of Ms. Marvel (in Avengers Annual #10), which is the very thing that Carol has been recovering from...
Rather than sort out some sort of awkward compromise ("why are you here?" "no, why are you here?"), they start having a superhero fight in the Pentagon. Storm and Wolverine somehow find the time to change into their costumes, which is not just one of those "where did they get the time?" moments, but is literally a terrible idea - as a "mutants infiltrate Pentagon" story becomes an "X-Men infiltrate Pentagon", aided by the guards overhearing them use the word "X-Man". If there were ever a job for X-Force, this was it. Mystique is captured (but she'll get out - she's that good), Rogue is subdued, the X-Men flee, and Danvers wipes those files. Not that it'll do them any good.
This would have been a perfectly good explanation as to how the X-Men became outlaws, but it's frankly incomprehensible as their reaction to it. In the end Kurt complains in a thought bubble
The X-Men will probably end up portrayed as the villains of the piece.
If Senator Kelly is any indication, the government is already paranoid about mutants. This will only make matters worse.
And since the X-Men have no official sanction, like the Avengers, they've no way of telling their side of things.
Yes, I'm quite sure that explaining how you were merely planning on illegally entering the government installation to remove the records on yourself would clear things up nicely.
While all this is happening, Corsair and Cyclops visit Havok and Polaris, and introductions are made. No mention is made of any other relatives - of either their mother or father - and neither of them were John Does - so presumably any grandparents are dead?