Some puzzles, if not completed within a short span of time (always less than a minute), will result in a game over. To ensure that the player does not get stuck by saving their game at a point from which they cannot possibly complete a puzzle in time, the game autosaves onto a separate save file at the beginning of each timed puzzle.
Late in the game, in Argentina, Ryan meets John Parker, the central character from Shadow of the Comet, and reveals the links between the two games. Narackamous, the main antagonist of Shadow of the Comet, also returns.
The game has a choice of two endings, though there is little difference between them.