The Security Officer defends both the UESC Marathon and the colony at Tau Ceti against an alien invasion by the Pfhor slaver race, with both help and hinderance from the three onboard A.I., Leela, Durandal, and Tycho. Durandal captures the player-character at the end of the defense and takes him to Lh'owon, the homeworld of the S'pht. There they seek an ancient weapon that the S'pht were creating to defeat the Pfhor at the time of their capture and enslavement. They find Thoth and the S'pht'Kr, but not before Durandal is caught and destroyed by Tycho and the Pfhor. At the very end of the second game, Durandal makes a glorious return and routes the Pfhor at Lh'owon, but not before the Pfhor fire the trih xeem, a weapon that causes Lh'owon's sun to go nova. The third installment in the series shows the player-character jumping through various timelines with the aid of the Jjaro to prevent the detonation of Lh'owon's sun and the release of the W'rkncacnter, a mythical being of chaos and disorder. The game ends with the successful completion of this mission and the christening of the player-character as Destiny.
Marathon begins with the Security Officer on board the shuttle Mirata coming in to land on the UESC Marathon, when Durandal, one of the three A.I. on the Marathon, decompresses the docking bay and orders him to abort. A Pfhor fighter teleports in just as you're leaving the shuttle, slightly delayed by having to don a vaccum-safe suit, and blasts the shuttle to bits. Durandal contacts you again, taunting you with your imminent death, when he suddenly loses interest and leaves you to enter the colony ship.
From there, you fall under the control of Leela, who believes that she's the only surviving A.I. from the intial assault of Pfhor fighters. She uses you first to engage the automatic defense systems of the Marathon. In the process, you encounter other alien species that have been enslaved by the Pfhor, including the S'pht and the Hulks, and you also discover that Durandal is very much alive and in a state of Rampancy. It is he, in fact, who sent out the message that brought the Pfhor to Tau Ceti to begin with, and he plans to use it as a tool to free himself from the bonds of humanity. Leela sweeps you up again and sends you on a mission to decompress part of the ship to prevent the Pfhor from reaching some of the more vital human-controlled areas, then prepares a message to send to Earth to warn them about a possibly imminent invasion.
As she beams the message out, Durandal steals you and teleports you to a section of the ship that Leela does not have access to. He plays mind games with you and you hear briefly from Tycho. Eventually Durandal tires of you and allows you to return to Leela, who has undergone extensive damage in your absence. Leela directs you to help protect some of her cores from the incoming assault, and Durandal helps you out as Leela begins to fail. He informs you of a new sector of Pfhor technology, the simulacrums. Despite your efforts to save Leela, she falls to the S'pht, who are able to interface with the computer systems of the ship and fight her directly. As she dies, Durandal takes over control of your situation entirely and throws you about the Marathon, projecting his hate for humanity onto you.
In doing so, he teleports you to the Pfhor ship and orders you to explore and kill. He sends you on a second trip to the Pfhor vessel on a mission to find Bernhard Strauss, his creator and one of the darker figures of humanity's history. Durandal discovers that the enslaved S'pht are hive-minded cyborgs who are controlled by royalty and that the Pfhor have duplicated royalty figures on their ship to maintain control and obedience of the S'pht. He sends you on a third trip to destroy these creatures and to both free the S'pht and end the invasion of the Marathon. During your trip over, Tycho falls to the S'pht and is then reborn by them and falls into allegience with them. He swears an oath to come after Durandal no matter the cost to pay him back for causing the death of millions of humans. Leela is also reanimated, having survived the attack by the S'pht and Durandal's own subterfuge by hiding herself. Durandal casts himself onto the Pfhor ship's computers because of the allure of the Pfhor technology, including their FTL drive.
The game ends with one last successful repulsion of the Pfhor. Durandal takes you with him on his ship, rechristened Boomer, Tycho departs with the retreating Pfhor, and Leela is left to rot on the remains of the Marathon. The colony on the surface of Tau Ceti was razed during the battle in space, and all humans were either captured or killed, with no unharmed survivors save for one resistance group led by Robert Blake. The final screen illustrates the discovery of Lh'owon by Durandal, bringing us to Marathon 2.
Marathon 2 begins with the Security Officer's release from stasis and teleportation down to Lh'owon, specifically to a water-processing plant. Durandal informs you that seventeen years have passed since you've last seen action as he teleports you about the surface of Lh'owon to strike at critical points in the Pfhor defense there. Apart from the water plant, you also hit a geothermal power plant, and some older S'pht-created duct work on the planet. He tells you that you're on Lh'owon to help the S'pht locate what their royalty had discovered in their last hours together here.
You destroy the Pfhor establishments at a defense center and at a landing site before moving on to one of their temples, where Durandal gives you a virus to implant into the Pfhor network there. The virus gives you temporary control of all the defense drones on the planet, and you take advantage of the chaos to gain an upper hand and slaughter the Pfhor garrison. The effect wears off quickly because the Pfhor have seen this trick before in the Nar rebellion years earlier. You explore the last bits of the garrison and analyze a Pfhor personality construct, who Durandal chides for not being truly self-aware and worthless to his cause.
Once you finish with the garrison you launch an assault on the old S'pht Citadel of Antiquity, where the elders made their last stand. You spend time first gaining entrance, then climbing the tower. You find nothing of true value at the top, so you search below in the basement of the citadel, going so deep as to encounter magma, and at the very bottom you find the secret that Durandal has been searching for: the eleventh clan of the S'pht, the S'pht'Kr, left Lh'owon long before it was invaded, and the elders had just reconstructed a way to call them back before their capture. If Durandal were to use this information, he would completely destroy the Pfhor invasion of Earth; unhindered S'pht are powerful allies.
Sadly, just as you find this secret, Pfhor renforcements that Durandal has been battling in the air for quite a while now gain the upper hand and he calls you back to his ship. Tycho is with them, and they attack mercilessly. Durandal is defeated, but before they can capture him he asks you to destroy him and his core, for an honorable death. As you break the last of the circuits, Tycho gains control of the ship and informs you that you were too slow, and that they had captured him just the same.
You are imprisoned for three months before Robert Blake of the old resistance finds you and breaks you out. He tells you that Durandal had been in touch with them during his last moments, and he instructs you to activate the various personality cells of Thoth, a S'pht A.I. long deactivated. Blake says that Thoth should help contact the S'pht'Kr and defeat the Pfhor once he is switched on. Once you activate Thoth, he takes you away from Blake and teleports you about Lh'owon, striking again at critical points in the Pfhor defenses while the S'pht'Kr travel to you.
Immediately after the S'pht'Kr arrive, Durandal unveils that he has escaped from Pfhor captivity after a fierce battle with Tycho that resulted in his crash onto one of Lh'owon's moons. Durandal etched an epitaph into the moon's surface, Fatum Iustum Stultorum. Blake ditches Lh'owon when he happens upon an unoccupied Pfhor carrier, and Thoth begins to help the Pfhor because of his obsession with balance. As you defeat the last of the Pfhor, Admiral Tfear orders their secret weapon, the trih xeem, to be fired on Lh'owon's sun. As Lh'owon fades into twilight for the last time, the S'pht say goodbye to their homeworld and Durandal sweeps you up again and takes off for a rogue star, just passing through our galaxy for the moment.
Marathon Infinity begins on one of the many orbital stations that the Jjaro left lying around the galaxy. Durandal speaks to you and tells you of the horror that was unleashed with the detonation of Lh'owon's sun. When the trih xeem was fired and Lh'owon's sun went nova, a W'rkncacnter was released from its gravity well and unleashed on the world. The Jjaro, watching the situation from afar, recognize the Security Officer for who he is and use their power to jump you across timelines until you arrive at a point at which you can both end the tyranny of the Pfhor and prevent the trih xeem from releasing the W'rkncacnter.
You immediately jump timelines and land in a universe where Tycho has control of you and is currently using you to cause a military coup of a starship. Once you eradicate a few areas of Enforcers and Troopers, you feel Durandal's wrath, and he cripples Tycho. Tycho teleports us down to Lh'owon to activate Thoth, who immediately recognizes your failure and sends you adrift to find another timeline.
In between timelines, you make contact with the Jjaro and dream of your life, and when you wake up, you are on a Jjaro scanning buoy in orbit of Lh'owon, with Durandal telling you to break circuits to cripple a Pfhor warning system. From there you commence crippling the Pfhor fleet by destroying powered-down Juggernauts and assaulting land bases on Lh'owon. Once again, you turn Thoth on just in time as Durandal begins to succumb in battle, and this new version of Thoth sends you off again.
In the third timeline, you find Durandal just beginning the assault on Lh'owon, but Tycho has already arrived and has his defenses in place. You are on Tycho's side this time, and you let the Pfhor deal with Durandal's preliminary attempts at combat as you work on crushing Robert Blake's resistance group planetside. At the end of this timeline, you crush Durandal in a very similar manner to how you assisted him in suicide in Marathon 2, and you physically drop down into his core to rescue a chip that contains his primal pattern. Thoth waits this time until the very last moment to pull you out, ensuring that you have the chip with you before pushing you out of the current timeline.
In the final timeline, Tycho is breaking you out of jail in exchange for you freeing him from the S'pht containment cell he's imprisoned inside. Tycho has you route some of Blake's forces while you're at it, and then drops you off at a Pfhor base, where you fight for your life. In the middle of the base is a teleportation device that leads down to an excavation site. Inside this area is a previously undiscovered section of Thoth, including both personality cells and a special uplink slot that you place Durandal's primal pattern chip into. Thoth and Durandal fuse and become godlike, but they cannot prevent you from being captured again by Tycho, who pits you in an area, coliseum-style, against some of Admiral Tfear's best men.
Marathon Infinity ends as the merged A.I. brings you up to the same star station you were in at the beginning of the game, this time equipped with superior knowledge and strength. It uses you to alter and engage the station's gravity field, previously used to warp entire planets between star systems. This time the gravity field is used to wrap around Lh'owon's sun and contain the inevitable nova, sealing the W'rkncacnter inside. Durandal says that he never sees any sort of sign that the W'rkncacnter exists in this time line, but you know better. The merged A.I. becomes Durandal again for a moment and he releases you from the tight grip that he has held on you over the past seventeen years and several lifetimes, allowing you to be free to alter the universe as you see fit.