15-year-old Kitty Pryde wakes up one day and finds herself able to walk though objects. She tries to ignore it, but finds that hard when she's approached by Jean Grey and a mutant trouble maker, who both say they know what she's going through and want to help her. Meanwhile Wolverine's old nemesis, Sabertooth, arrives in town - looking for trouble.

Magneto steals plans for a top-secret project that produced super soldiers. Wolverine worked on it during World War II.

X-Men and the Brotherhood deal with the aftermath of the world finding out about mutants. The Institute is blown up, and Mystique posed as Prof. X to blow it up. Some of the X-Men and Brotherhood are captured, leaving the mutants that escaped to find them and the Professor.

Rogue and Wolverine duck a squad of soldiers when the nationwide alert goes out against mutants, while Storm and Beast go into a meeting of Congress to defend themselves. Meanwhile Juggernaut goes on a rampage and the X-Men feel obliged to take him down.