Mystique wanted greater power.  In recent years the heroes had found many ways to see beyond her shape-shifting abilities.  Wolverine knew her scent, Xavier could scan her mind, even Stark and Richards had technology that made her shape shifting virtually useless.

To get greater power she sought out Fabian Cortez.  Cortez could bolster another mutants power.  He promised her that not only would her disguise be perfect again, but she could copy the powers of other mutants.

Unfortunately there was a side-effect Cortez did not foresee.  Her disguise became so absolutely perfect that she even fooled herself.  Mystique spent many years actually believing she was: