There are at least a half-dozen plotlines running through this book, which doesn’t officially tie into Operation: Zero Tolerance but, of course, does tie into it.
The main story here is Sabretooth shedding his containment collar, attacking several team members, and escaping. He heads for Trevor Chase’s house–to kill the boy.
He just wants to kill him because Mystique likes him, and Sabretooth wants to annoy her. He murders Trevor’s sibling, but Trevor escapes. Sabretooth is savage in this comic.
Mystique protects Trevor.
Val Cooper and Mystique take the injured X-Factor members to the hospital, and then the two argue. Mystique feels Val is a government stooge who is only pretending to care about mutantkind while she exploits them as X-Factor (remember, Mystique also wears a dampening collar), while Val accuses Mystique of being a purely self-interested villain.
They’re both right.
Federal troops arrive (because remember the whole lot of these folks are on the run), but so does Havok–leader of the new brotherhood. He saves the X-Factor members and takes them to a safehouse to provide more medical care.
Sabretooth then turns on his government employers, hunting them down with intent to kill–but in the middle of his hunt, he’s attacked by Omega Red, who wants to capture him for a reward from the daughter of a man Sabretooth killed.
Omega Red fails.
At the same time, Mystique uses her powers to trick a Senator into launching an attack force against Sabretooth.
So Sabretooth is being hunted by multiple forces at this point.
The next couple issues focus on the computer-generated AI sister of Bishop, Shard. When Sabretooth escaped X-Factor, he shredded Shard’s pixilated body. This apparently sent her intelligence back to her alternative future (ugh), and we’ll be getting a few issues that take place in that timeline (double ugh).