New X-Men by Grant Morrison #1

Plot

Sixteen million mutants dead...and that's just the first step in Cassandra Nova's genocidal plans. With an army of evolved Sentinels primed for annihilation, Nova will stop at nothing to see every mutant exterminated from the planet. Led by Professor Xavier, the X-Men have always sought an end to the ongoing strife between mutants and humans - hoping to one day unite the two species in peaceful coexistence. But the time for dreams is past. Now, their entire existence is under direct attack. Now, it is time for the X-Men to fight.

Collecting NEW X-MEN #114-117 and ANNUAL 2001.