In the middle of January Xavier's School for Gifted Students was attacked in the dead of night. Both mutant and non-mutant alike fought to lend a powerful blow to the mutant community by taking out the school. They did not expect the battle they would be faced with and many were lost that night. Since then, under the leadership of Ororo Munroe, the staff and students at Xavier's have struggled to find normalcy once more. The mansion is being repaired slowly, security enhanced, and students are finding comfort in consistent classes once again. But there are darker things looming just out of sight.

In the space of one day, Magneto, who was at the mansion to help a struggling Lorna Dane, has disappeared along with the green-haired girl. Scott Summers, long thought dead, has returned to find his one-time home still in a state of partial ruin, his lover gone, and his father-figure dead. With shifts in command and mutants losing control of their powers due to cures wearing off, what else will the residents of Xavier's have to face. Is the New Brotherhood still a threat, perhaps an even bigger one now with Magneto on the loose? If Scott is somehow alive, could it mean the professor lives somewhere, too?