Mark Pellegrino returns in his role as Jacob , the mysterious figure in charge of the island , while Titus Welliver also reprises his role as the mysterious unnamed character , known only as `` The Man in Black '' , who appeared to be antagonistic to him in the season 5 finale . Mark Pellegrino reprises his role as Jacob , the mysterious figure in charge of the island , while Titus Welliver also reprises his role as the mysterious unnamed character , known only as `` The Man in Black '' , who appeared to be antagonistic to him in the season 5 finale .