The story — titled "Blood Tides of Lh'owon" — begins as if the events of Marathon 2 never happened. The central threat is the W'rkncacnter: an ancient entity of pure chaos, sealed inside Lh'owon's sun by the Jjaro eons ago. The Pfhor have fired their "early nova" device at that sun to destroy it, which risks releasing the W'rkncacnter into the world. The player jumps between alternate realities — apparently caused by Jjaro technology or the W'rkncacnter's own chaotic nature — attempting to prevent the release before it becomes irreversible. The opening places the player under Durandal's command; almost immediately, a reality shift moves them to a world where Durandal never rescued them at the end of the first Marathon, putting the Pfhor-controlled AI Tycho in charge of their fate instead.