In 1715, twenty-eight-year-old Lincoln is imprisoned aboard the Spanish galleon San Telmo, shackled in the darkness of its hold and surviving on scraps while the ship sails along the coast of Tortuga. Despite his captivity, Lincoln remains calm and sarcastic, patiently studying his surroundings for a way out. His opportunity arrives when the galleon is attacked by pirates. Using the chaos of the battle and the weakened condition of his rusted restraints, Lincoln manages to break free and escape the hold. But freedom proves just as dangerous as captivity. Emerging onto the deck, Lincoln finds himself caught in the middle of a brutal naval battle between the Spanish and pirates. As cannon fire tears the ship apart and pirates begin boarding, he spots a mysterious and formidable woman among them. Dressed in a weathered brown coat and armed with pistols and a cutlass, she moves with the confidence of someone who has survived countless battles at sea. With the San Telmo falling apart around them, Lincoln's escape has unexpectedly brought him face-to-face with a woman who may completely change the course of his life.

In 1944, young Charles Xavier discovers Raven, a blue-skinned shapeshifting mutant who has been posing as his mother, and rather than fear or reject her, he welcomes her into his home, beginning an eighteen-year bond as adopted siblings. By 1962, Charles has earned his PhD at Oxford and dedicated himself to understanding human mutation, while Raven works at a local pub and struggles to control her shapeshifting. Charles meets Amy, a woman with heterochromia, and recognizes her as a mutant, enthusiastically encouraging her to embrace her difference. Later that night, Charles and Raven encounter Lincoln Grey, a mysterious young man who has read Charles's research and reveals that he too is a Mutant. though his strange presence and enigmatic abilities suggest there is far more to him than meets the eye.