Halo: Combat Evolved
- Main article: Halo: Combat Evolved
- The Marathon AI Durandal, is named after a mythical sword. Cortana's namesake is the sword Curtana, which bears the inscription: My name is Curtana, of the same steel and temper as Joyeuse and Durendal.
- Sometimes Grunts or Marines will shout "They're everywhere," similar to the BOBs of Marathon.
- Echo 419's pilot, Carol Rawley, has the callsign Foe Hammer, a possible reference to the level of the same name in Marathon: Infinity.
- Marathon has a level named "If I Had a Rocket Launcher, I'd Make Somebody Pay." In Halo: Combat Evolved, the level Assault on the Control Room's final chapter is called "If I Had a Super Weapon..."
- Light markers- The Covenant light markers in Two Betrayals bear a resemblance to Pfhor staves.
- MJOLNIR- There are Mjolnir Mark IV cyborgs in Marathon, there is Mjolnir Mark V battle armor in Halo.
- On the back part of the Halo rocket launcher it says "SPNKR" which is a reference to the Rocket launcher of Marathon, the "SPNKR X-18 SSM Launcher."
- The Flamethrower in Halo PC has a similar name to the flamethrower found in Marathon: "7057 = TOZT."
- The Plasma Pistol is much like the Fusion Pistol from the Marathon series, which also shares a vibrating overcharge shot.
- Grunts are similar in design to the generic Pfhor fighters, both being gray-skinned with gangly limbs, with unprotected heads but wearing masks over their mouths (though this is a loose comparison).
- Private First Class Chips Dubbo on the level 343 Guilty Spark may say "Oh God, I recognized that one. That was Bob!" in reference to Marathon's Born on Boards (BOBs).
- John-117's Spartan Number is 117. In Marathon: Infinity, there was a hidden multiplayer map called Hats Off to 819 (named after fan Hamish Sinclair, H=8, S=19). 819 divided by 7 is 117. Hats Off to 819 is also the name of an achievement in the Xbox Live Arcade port of Marathon: Durandal.
- The Bumblebee pilot in the Halo cutscene wore a helmet similar to that of the Marathon Protagonist.
- The marine boots and chest plates were inspired by the ones worn by the Marathon Protagonist.
- The campaign begins with John-117 awakening from cryo sleep after a massive battle, much like it did in the beginning of Marathon 2: Durandal, where the Protagonist woke up after cryo sleep from a massive battle.
- In the game's tags, Master Chief is referenced as "Cyborg." Unggoy also appear to occasionally refer to John-117 as "Cyborg."
- In The Pillar Of Autumn, if you shoot Captain Keyes (or any other human on the bridge) after you get your pistol, Cortana will announce that John-117 has gone rampant, like Durandal went rampant in Marathon.
- The front cover of the game has the Marathon logo between the "a" and the "l" of the word Halo. This is also seen in the logo of the cancelled Halo DS, as well as various novels based on the series.
- When selecting a difficulty in campaign mode the Marathon logo is visible on the shield (that has a Combat Knife (or two Combat Knives) and an Elite skull over it depending on the difficulty).
- 343 Guilty Spark has the Marathon symbol around his eye and on his eye in the first and third game.
- Captain Keyes has the ship's Emblem of the Pillar of Autumn on his uniform, which is the Marathon logo.
- Captain Keyes has the Marathon logo on his pipe.
- The Control Room's (from the level Assault on the Control Room/Two Betrayals) main chamber, when viewed from the top, is shaped like the Marathon logo.
- Pillar of Autumn - The Marathon logo can be seen on both sides of the ship.
- Warthog- The Marathon logo can be seen on the dashboard panel.
- The Silent Cartographer- The center of the island is shaped like the Marathon logo.
- Halo PC Loading Screen- If you brighten the gamma on Halo PC a lot, you can see what looks like the Marathon symbol etched in the background of the first loading screen.
- Spirits - The Marathon logo is on the front of the cockpit.
- On the Plasma Grenade, the Marathon logo is visible on the orange part.
- The Halo PC map Danger Canyon is laid out in a way that resembles the Marathon logo, with the outer cliff being the outer circle, the caves and tunnels being the inner circle, and the Cliff wall separating the bases being the line at the bottom.
- Main article: Halo 2
- In the opening cinematic of the level Cairo Station, Lord Hood says "United Earth Space Corps," Marathon features the Unified Earth Space Council, both share the UESC acronym.
- In the first cutscene of the game, one can see a Marathon-Class Cruiser near Cairo Station.
- The multiplayer map "Foundation" is based on the Marathon "Thunderdome" level.
- The multiplayer map "Gemini" is based on the Marathon level "Duality." This is supported by the map's description, mentioning the "ancient duality of the Covenant..."
- The Elite rebellion against the Covenant parallels similar events in the Marathon series. In Marathon, Durandal convinced a group of S'pht to rise up against the Pfhor who enslaved them; and after Durandal's disappearance in Marathon 2: Durandal, the rebel S'pht found themselves stranded together with a group of humans on a hostile world (similar to the Elites' predicament on Delta Halo).
- The player's main goal in Halo 2 is to stop the Covenant from inadvertently destroying all life in the galaxy with the Halo installations; in Marathon: Infinity, it was to prevent the Pfhor from inadvertently releasing a galaxy-destroying chaos being.
- Some Marines can be heard saying "Eat it, boy," possibly referring to the Marathon 2: Durandal level named "Eat it, Vid Boy!"
- There is a sub-chapter in The Great Journey named "Delusions and Grandeur." Marathon: Infinity has a network level named "Delusions of Grandeur."
- Sometimes Marines say "Thank God it's you," which is what the Simulacrum BOBs say in Marathon.
- The Mausoleum Suite was based on the Marathon 2: Durandal theme song.
- The difficulty shield has the Marathon symbol.
- The Marathon logo can be applied as a 'decal' to the multiplayer avatar/flag.
- The Marathon symbol is also used in the Halo 2 Multiplayer online as a gamer tag.
- The Marathon logo can be seen on the Doors on the level Regret.
- If you get outside the level Burial Mounds, look at the rubble by the "ribs" a large piece of debris is engraved with the logo.
- On the map Midship, you can see the Marathon symbol on Africa (best viewed with scope).
- The Enforcers' shields make up the Marathon symbol.
- If you melee with a shotgun, you can see a Marathon symbol on the silver casing.
- On Headlong, in the building which houses mostly human weapons, if you look at the second floor from above it makes out the Marathon logo.
- If you look at the multiplayer map "Ivory Tower" from above, you will see that the circular courtyard and the small ditch which the water runs along makes up a Marathon logo.
- The Oddball skull has the Marathon logo in its eye socket.
- In the level Uprising, when you get to the final cutscene at the end and the level The Great Journey begins, go back to the door and you can see two Marathon logos on the door. Marathon logos can also be found on several other doors in this level.
- In the level The Great Journey, there are two Marathon logos on the large door by the part with the two Wraiths.
- The multiplayer level Containment has 2 Marathon symbols on each door at the back of both bases.
- The Halo 2 savegames, when viewed in Windows Explorer, have the Marathon Symbol over the basic file symbol.
- Main article: Halo 3
- The Campaign begins with John awakening from a massive battle in an enemy space station in the presence of his allies near a water treatment. This is similar to the beginning of Marathon 2: Durandal, in which the Protagonist awakens from a massive battle on an enemy planet to continue fighting with his allies in the Waterloo Treatment Plant.
- On the last cutscene of the level Floodgate, when Thel 'Vadam is bringing UNSC weapons, a Flamethrower and a Rocket launcher, are held in the same position as the Cyborg's picture from Marathon: Infinity.
- There is an achievement for accessing all the terminals in the campaign, called Marathon Man.
- In the E3 2007 trailer, and on the level The Storm, boxes marked TRAXUS can be seen. Traxus IV was the name of a famous rampant AI in Marathon's universe.
- Additionally, in the level The Storm, Traxus IV can be seen etched on the glass panels in the warehouses.
- The Brute Mauler was probably based on the shotgun from Marathon, which was also dual-wieldable.
- There is a Marathon: Infinity level editor called Forge. Halo 3 shares that name of its map editor.
- At the end of the game, the rear section of the ship Master Chief is on, the UNSC Forward Unto Dawn, drifts towards Requiem as the Marathon logo flashes on the surface.
- Alex Seropian once stated that John-117 and the main character of Marathon were the same character. Bungie has since denied this, with Seropian explaining that they weren't the same person, but different reincarnations of the same character.
- The way the Brute holds the marine captive on Sierra 117 is possibly a reference to the L'howon chapter screen.
- Some Marines sometimes say "Thank God you're here," which may refer to when BOBs say "Thank God it's you!"
- On July the Fourth, the phrase "B-B-Q at BOB's Place!" which can be seen on the Forerunner wall of Valhalla which is a reference to BOB-B-Qing, when you kill many of the BOBs in Marathon. BOB-B-Q is also the name of an achievement in the Xbox Live Arcade port of Marathon: Durandal.
- In Marathon, the first level (Arrival) shares its name with Halo 3's opening cutscene.
- Elite Combat Forms Occasionally Say "Melancholia, Anger..." a reference to the 3 stages of Rampancy, a reference to the error with A.I. in Marathon.
- Unggoy occasionally scream "He's/They're everywhere!" referencing the BOB's line in Marathon. Sangheili also appear to say this line on very rare occasions.
- The personnel in Crow's Nest wear uniforms like those of the BOB's from Marathon.
- The design of the golden hologram on Epitaph was inspired by the S'pht Compilers from Marathon 2: Durandal.
- On the Mythic multiplayer map Heretic the Marathon symbol is visible on a side-of-the-room walls' shield.
- Rampancy is the name of an emblem in Halo 3's multiplayer. This is in reference to the error in Marathon A.I.
- Covenant communication nodes make up the Marathon Symbol.
- The weapons are often decaled with Marathon symbols.
- The Marathon symbol can be seen in the planet in the sky on the level Snowbound.
- When you look at a High-Resolution screenshot of John's weapon from the Halo 3 Announcement Trailer you can see a Marathon logo. Confirmed by KP .
- The BR55 Heavy Barrel Service Rifle has the Marathon logo on its optical sight.
- The Brute Mauler has the Marathon Symbol on its hilt over where you hold the weapon. You may need to look down in light to see it properly.
- The M6G has the Marathon logo on the grip near the back.
- 343 Guilty Spark's eye, which makes the shape of the circle in the Marathon Logo, also has the full logo inside the eye.
- On the Spartan Insignia, there is a gold Marathon logo.
- The control panels on the elevators on the level The Covenant have the Marathon symbol on them.
- On the level Tsavo Highway, the Marathon logo appears on the sides of the CCS-Battlecruiser flying overhead.
- The MA5C has a Marathon logo on its butt plate.
- Some ODSTs have the Marathon symbol on their chest armor.
- The Marathon Logo can be seen on the launch bays of Covenant Capital Ships. This is most easily seen by traveling toward the one outside the hanger in saved films on Crow's Nest.
- In the settings menu, the picture of the Spartan when appearance is highlighted has the Marathon logo on its shoulder.
- The Security Helmet in Halo 3 resembles the helmet that the main character of Marathon (who works in security) wears. It also has a Marathon symbol on its forehead.
- There is a distorted Marathon symbol on the table of the Shadow of Intent's Conference Room.
- Just like in Halo: Combat Evolved, the Control Room of Installation 08 forms the Marathon symbol.
- The elevators on The Covenant (and possibly The Ark as well) have the Marathon symbol on their control panels.
- The blue objects on Drones have a Marathon logo on them.
- The yellow hologram on the multiplayer map Epitaph has a Marathon logo on the circular part.
- The Marathon Logo can be used as an Xbox Live Gamer Picture.
- In Halo 3, you can use the Marathon Logo as your emblem.
- As with 343 Guilty Spark, if you go on the Forge level creator and turn into the monitor, have a friend look at your eye closely or go back in theater mode, and there is a Marathon symbol in the eye and the eye is shaped similar to a Marathon symbol.
- The difficulty icon shield has the Marathon symbol on it.
- The center of the Halo 3 multiplayer map Guardian is similar to the Marathon logo.
- In the multiplayer map, Cold Storage, the Marathon symbol can be found on the ceiling-mounted monitor's eye (being a copy of the Monitor model).
- In the level The Ark, there is a Marathon Logo at the Cartographer which can be seen if you look from above in Theater. The Cartographer and the glass down below makes the logo.
- The Recon helmet has Marathon symbols on the ears.
- Marathon symbols reflect off of the surfaces of the interior walls of the ship in Heretic.
- There is a Marathon Logo on the back of the Assault Rifle.
- The Marathon Logo is visible in the back of the vidmaster achievement icons.
Halo 3: ODST
- Main Article: Halo 3: ODST
- The avatar used to represent the AI Tycho from Marathon was added to the list of emblems under the same name as the AI. It is also the second emblem to be added to Halo with affiliation to Marathon.
- At the very start of Uplift Reserve it is visible.
- It is visible on the Rookie's backpack. Also, some bodybags have it.
- It is also visible on Sergeant Johnson's backpack.
- If you look closely at Dare, a Marathon symbol is visible on the bottom of her backpack.
- Before you enter the elevator in Coastal Highway, if you jump above the circular structure near the door, it makes the shape of the Marathon symbol.
- The Marathon logo appears on the difficulty icon shield.
- The Marathon logo can be used as your emblem.
- Main article: Halo Legends
- Main article: The Babysitter
- A symbol is seen on a rock when the whole waterfall is visible, as well as inside the waterfall at the base.
Bungie avoided the use of the Marathon symbol in Halo: Reach, presumably due to property rights issues with Microsoft. The symbol was removed from the emblem gallery, the difficulty icon shield, the hull of the Pillar of Autumn, and replaced with the Seventh Column symbol on Captain Jacob Keyes' ID patch (These changes are also present in Halo: Combat Evolved Anniversary, along with removing the Marathon logo from 343 Guilty Spark's eye). The one place the symbol can still be seen is in the eye of the Forge Monitor.
- On one of the wallpapers of Halo Reach, where Reach is visible in the background, in the top left corner of the planet a Marathon symbol is visible as a river.
- Rare, yellow-armored Sangheili Rangers encountered in the game are referred to as "BOBs" in Bungie.net game stats. BOBs are a type of human allies in the Marathon series.
- At the beginning of the credits, it says "We'll see you starside." This quote comes from BOBs in Marathon 2: Durandal.
- The Marathon logo appears in the turret of the Wraiths.
- The Marathon logo is in the map Reflection.
- The Marathon logo is spotted several times in the level Nightfall.
- In Nightfall, the title of a chapter is "Let Sleeping Dogs Lie..." The quote is used in Marathon, but is actually from Pathways Into Darkness. The full quote is "Let sleeping dogs lie, let sleeping gods die."
- Several challenges are quotes from Marathon, such as "House of Pain," referring to a Marathon 2 : Durandal Netmap.
- The Marathon logo is visible in the small of the Elite's back. It is illuminated by a small, randomly colored glow.
- In the city of New Alexandria, there is a building called Traxus Tower, referencing Traxus IV from the Marathon series.