Myst III: Exile

Exile begins ten years after the events of Riven, when the player arrives at Tomahna, the home of Atrus and his wife Catherine. Atrus is a scientist and explorer who has mastered an ancient practice known as the Art: he can create links to different Ages by writing special books. This ability was developed by an ancient civilization known as the D'ni, whose society crumbled after the D'ni city was devastated by a plague. Atrus calls the player to his home to display his newest Age, Releeshahn, which Atrus has designed as a new home for the D'ni survivors.
As Atrus and the player prepare to leave for Releeshahn, a mysterious man appears in Atrus' study and sets it on fire, stealing the Releeshahn book. Following the thief via the book he left behind, the player arrives at J'nanin, an Age that Atrus had written long before as a way to teach the Art to his sons. Because the fire has caused considerable damage to the J'nanin book, Atrus cannot accompany the player.
The thief is named Saavedro. Twenty years earlier, Atrus' wayward sons Sirrus and Achenar destroyed Saavedro's home Age of Narayan and trapped him on J'nanin. Saavedro believes his family is dead and swears vengeance on Atrus, unaware that Atrus has imprisoned his sons for their crimes and that Saavedro's family is still alive. The game can end several ways depending on the player's actions. In the most ideal scenario, Saavedro returns to Narayan peacefully after giving back the book of Releeshahn. Other endings result in Saavedro destroying Releeshahn or killing the player; another option allows the player to leave Saavedro trapped forever.