Set in the year 2794 A.D., Marathon places the player as a security officer, dispatched to respond to a distress signal sent from the enormous human starship called the U.E.S.C. Marathon, orbiting a colony on the planet Tau Ceti IV. Throughout the game, the player attempts to defend the ship (and its crew and colonists) from a race of alien slavers called the Pfhor. As he fights against the invaders, he witnesses interactions among the three shipboard AIs (Leela, Durandal and Tycho), and discovers that all is not as it seems aboard the Marathon. Among other problems, Durandal has gone rampant and appears to be playing the humans against the Pfhor to further his own mysterious agenda.
Seventeen years after the events of the first game, in Marathon 2: Durandal, the artificial intelligence, Durandal, sends the player and an army of ex-colonists to search the ruins of Lh'owon, the S'pht homeworld. Lh'owon was once described as a paradise but is now a desert world after first the S'pht Clan Wars and then the invasion by the Pfhor. He does not mention what information he is looking for, although he does let it slip that the Pfhor are planning to attack Earth, and that being on Lh'owon may stall their advance. Marathon 2 brings many elements to the game that can be considered staples of the series such as: a Lh'owon-native species known as F'lickta, the mention of an ancient and mysterious race of advanced aliens called the Jjaro, and a clan of S'pht that avoided enslavement by the Pfhor - the S'pht'Kr. At the climax of the game, the player activates Thoth, an ancient Jjaro AI. Thoth then contacts the S'pht'Kr, who in turn destroy the Pfhor armada.
Marathon Infinity, the final game in the series, includes more levels than Marathon 2, which are larger and part of a more intricate plot. The game's code changed little since Marathon 2, and many levels can be played unmodified in both games. The only significant additions to the game's engine were the Jjaro ship, multiple paths between levels, a new rapid-fire weapon that could be used underwater, and vacuum-enabled humans carrying fusion weapons (called "Vacuum Bobs" or "VacBobs"). The player traverses multiple timelines, attempting to find one in which the W'rkncacnter is not freed. In one timeline, the player is forced to destroy Durandal, and in another Durandal merges with Thoth. At the end of the game, an ancient Jjaro machine is activated that keeps the W'rkncacnter locked in the Lh'owon sun.