The game is mostly set on the fictional planet of Lh'owon, homeworld of the S'pht, and once again the player takes the role of a shipboard security officer from the Marathon.

The unofficial Aleph One community enhancement, built on engine source opened by Bungie in 1999, allows the game to be played on many other platforms.

The entire game including assets was released for free to the public by Bungie in 2005, now commonly bundled for distribution with Aleph One.

Durandal, one of the three AIs from the colony ship UESC Marathon, sends the player and an army of ex-colonists to search the ruins of Lh'owon, the S'pht home-world.

In that game the UESC Marathon is in orbit around Tau Ceti's fourth planet, where a colony is being formed.

The story begins when the security officer is awakened from stasis and informed that he was abducted moments before Durandal departed from Tau Ceti space.

Durandal teleports the security officer to the ancient citadel of antiquity, where the S'pht made their last stand against the Pfhor in the final hours of the invasion.

While the security officer makes his way far into the citadel, Battle Group Seven of the Pfhor fleet arrives and engages Durandal's ship.

Durandal, not wanting to "end up like Leela", has the security officer destroy his core logic centers to avoid capture by the Pfhor.

Tycho brags of the brutal aftermath of the Tau Ceti invasion, in which all colonists and crew of the Marathon were vaporized by a Pfhor fleet shortly after Durandal left.

Durandal had learned that the S'pht were worshipers of the Jjaro, an ancient and powerful race of beings that vanished long ago and possessed the ability to bend space.

With this done, Thoth and the security officer activate an ancient communication array that contacts the S'pht'Kr, a clan of S'pht that left Lh'owon shortly before the arrival of the Pfhor.

Durandal informs the player that an impending invasion of Earth has been halted permanently, and the now-free S'pht have gathered all they can from Lh'owon and have left the doomed system.

The game's interface has been changed, with the view of the player being much wider than in Marathon (which was smaller to improve game performance) and now taking up the lion's share of the screen, displaying the player's health and oxygen bars horizontally at the bottom of the screen rather than on the left vertically above the motion sensor.

For instance, the civilians, completely defenseless in Marathon, now carry pistols they can use to defend themselves (and with which they will shoot the player if attacked).

The Marathon 2 engine offered performance gains on some machines, in addition, to support for deeper color depths and higher resolution sound.

A free (with in-app purchases) Aleph One-based port with Bungie's permission, to the iPhone and iPad, was made by Soli Deo Gloria Productions.

[3] The game also supports 16:9 screen resolutions, high-definition output at 60 frames per second (compared to the original 30) as well as upgraded models and graphics,[4] support for 8-player co-op mode over Xbox Live, several international versions, and a new game mode called "Survival" where the player is given a large amount of weapons and ammo and must defeat endless waves of enemies, earning points for effectiveness and taking minimal damage, with high scores shared over Xbox Live.

[5] The only feature from the original game not present is the ability to save films, due to limits on user storage provided by Xbox Live[6] and a bug caused by lag.

"[9] In 2008, Freeverse worked on a downloadable expansion for the game, consisting of multiplayer maps converted from Marathon Infinity.

The trilogy itself was released by Bungie as freeware in 2005, and can be downloaded at the link below along with a copy of Aleph One in order to play the game on modern versions of Windows, macOS, Linux, and numerous other platforms.

As with all Bungie titles before the fully crossplatform Myth: The Fallen Lords, Marathon 2 achieved lifetime sales below 200,000 units by 2002.