It picks up right where DoR left off. Scott and Mystique are at each other's throats when suddenly the area is stormed with police officers and soldiers who try to arrest them. All hell breaks loose as the mutants use their powers to escape. Berzerker takes charge of the New Mutants and leads them into the city. The Brotherhood flee, and Storm flies off with Scott. In an amusing sequence, Kurt, Jean, Kitty, and Bobby flee in a cop car.
Later, they all reunite at a lookout point. Mystique says they have to join forces in order to rescue their teammates from the military, and assumes control of the group, threatening to not reveal Xavier's location if they question her. Nick Fury appears, and gives the X-Men the location where their friends are hidden. Mystique then sends Todd and Wanda off to New York to make sure that Magneto died when the Sentinel crashed into the building. They then discover from watching news reports that Pietro rescued Mags just before the robot hit the building. Wanda is not pleased. Also, we see that Todd has a crush on Wanda, and his flirtations with her are hilarious.
Meanwhile, the New Mutants witness all the Anti-Mutant paranoia that's surfaced since they were exposed. Berzerker leads them into the sewers, saying he knows a place where they can seek shelter. They then encounter the Morlock Caliban, who takes them to a place unknown.
After stealing a helicopter, Mystique and the X-Men infiltrate the military base. Iceman and Shadowcat try to turn off the alarms, but set it off accidently. The X-Men and Avalanche are able to use their powers to get past the guards, while Mystique and Nightcrawler free their friends. As they make their escape, Scott traps Mystique in a corridor as the soldiers are coming, demanding that she reveal Xavier's location. She refuses, and says he doesn't have the guts to leave her there. He does.
In the end, the Brotherhood and the X-Men go their sperate ways, and the reunited team looks out into the horizon, hoping they can find a way to prove to humanity that they are the good guys.