I can sort of see how that arose: it has an anomalous chronological placement. The Chronology Project awkwardly puts it just before the last page of Uncanny X-Men #168 (it doesn't quite work as Kitty Pryde's codename is "Ariel" in this, but that's easier to overlook than the presence of Wolverine and Cyclops - tricky continuity is nothing new), so let's go with that here.
The basic story is that William Stryker, a former army sergeant, hates mutants (his child was one: he killed it and his wife). After a phase of drunkenness, he read an article by Xavier, got religion, and set up his own ministry: the Stryker Crusade.
Stryker is the latest in the line of humans who are afraid of mutants and want to wipe them out, but the first to do this without the aid of giant robots, and the first to be explicitly religiously motivated. There's a little bit of anti-evolutionary rhetoric in him, and he's the first person to ever ask why there are mutants, anyway? He plans to brainwash Xavier, and use his brain and a modified Cerebro as the instrument of destruction. He fills out Madison Square Gardens and gets a live TV broadcast of his finale, so the X-Men can't very well intervene. So they send Magneto to disrupt proceedings, who has less of a PR image to maintain, while they slip in the back.
Like Magneto's revelation in #150, the climax is someone threatening violence against young Pryde. In this case, though, Stryker shows no compassion, and has to be forcibly stopped from shooting her, by a cop. He'll be serving time for this.
The entire thing is dark and moody, both tonally and graphically. There's no Comics Code Authority logo on the front of this, and Claremont has taken full opportunity of it, by having Anne call someone a "bitch". Ah. This is where I should be talking about the use of the N-word, isn't it. I'm not sure there's much new for me to say. It is difficult to compare a madey-uppy slur like "mutie" with a real life word with a century or more of derogatory usage. It has something of the "Die Cis Scum" about it - in form it is abusive, but there's no real power behind it. It feels cheap, especially in something that's presenting itself a more classy "graphic novel". But the narrative doesn't pretend that Kitty didn't cross the line - Colossus immediately makes excuses for her. Because she was wrong.
Apart from the basic premise of Stryker and a copy of Cerebro, X2 also picks up on the temporary alliance of the X-Men and Magneto. This is the first time we've had this in the comics, and I don't think it quite works. Not Magneto's characterisation so much, but the way the X-Men just accept it. This is the first time we see them find out his name is "Magnus", or that he and Charles are "old friends". If X-Men really is a soap opera at this point, much drama could be made out of these things. And yet, nothing. This is mostly explicable by this being a graphic novel - it just wants to tell its story, not further the ongoing one.
I leave you with an exchange between Cyclops and Magneto.
MAGNETO Contentment breeds tranquillity. Discontent, rebellion. Therefore, I shall ensure the one by eliminating the root causes of the other: hunger, poverty, disease, war. The freedoms lost will not be noticed, even in the most libertarian of states. And the material benefits should more than balance the scales. CYCLOPS Anyone can create an utopia for a single generation, Magneto; the trick is making it last. Who preserves your dream after you're gone? MAGNETO You, of course, Cyclops. And the X-Men. Why do you think I want you by my side?