S6E15 · Across the Sea

Claudia, a pregnant castaway, has her twins, Jacob and the Man in Black, delivered by an island native who kills her and raises them as her own. She uses her power to prevent them from harming each other and shows them the island's "heart," intending to make one of them its protector. Claudia's ghost tells the Man in Black the truth about his parentage, and he goes to live with her stranded shipmates. Thirty years later, they are trying to leave by digging where they find pockets of electromagnetism, with the Man in Black building a wheel around one of these spots.

His mother finds out, fills the hole, and kills his people, while also making Jacob the island's immortal protector. The Man in Black kills her, so Jacob throws him into the heart, destroying his physical form and turning him into smoke. Jacob places his and their mother's body at rest in a cave, where they are discovered by Jack two thousand years later.