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- Captain Keyes has the Marathon symbol next to his name tag. His pipe also has the Marathon logo on it. This is only in Halo: CE.
- Monitors, such as 343 Guilty Spark, have a single "eye" with the appearance of the Marathon logo.
- Control Room - The Control Room main chamber, when viewed from the top, is shaped like the logo.
- Difficulty Shield - The Marathon logo appears on the Easy Shield.
- Pillar of Autumn - The Marathon logo can be seen on the side of the ship.
- The Silent Cartographer (level) - 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.
- Spirit - The Marathon logo is on the front of the cockpit.
- The dot on the I in the Bungie logo resembles the circle in the Marathon logo.
- On the plasma grenade the marathon logo is visible on the orange part.
- The marathon symbol is also used in the Halo 2 Multiplayer online as a gamer tag symbol.
- Doors - The doors on the level "Regret" in Halo 2 bear the Marathon logo.
- If you get outside the level Burial Mounds, look at the rubble by the "ribs" a large piece of debris is engraved with it
- The Enforcers shields make up a 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 a marathon logo in the eye.
- When you look at a High-Res screenshot of John's gun from the Halo 3 Announcement Trailer you can see a Marathon logo. Confirmed by KP 
- The BR55HB SR Battle Rifle has the Marathon logo on it's optical sight.
- At the end of the game, the rear section of the ship Master Chief is on, the UNSC Forward Unto Dawn, drifts toward a planet as the Marathon logo flashes on the surface. Alex Seropian once stated that Master Chief and the main character of Marathon were the same character. Bungie has since denied this, but the ending of the game may in fact connect them.
- The M6G has the Marathon logo on the grip near the back.
- The Marathon logo can be seen on a hologram, used to activate the elevators in the level, The Covenant.
- 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 buttplate.
- In the mission Cortana, in the spot where you can get the flamethrower where the dead ODST is, and on the center of the ODST's stomach armor there is a marathon symbol
- The Marathon Logo can be seen on the side of covenant capital ships. This is most easily seen by traveling toward the one outside the hanger in saved films on Crows Nest.
- In the settings menu, the picture of the spartan when appearance is high-lighted, has the logo on its shoulder
- In the Diorama on Halo3.com, the video Testimonial:Enemy Weapon, when the camera centres on a sniper rifle, a closer look brings up a Marathon symbol.
- The center of the Halo 3 mutiplayer map Guardian is similar to the Marathon logo
- The MA5C has a Marathon logo on its buttplate
Halo: Combat Evolved Edit
- Cortana - The Marathon AI Durandal, is named after a mythical sword. Cortana is a sword which bears the inscription: My name is Curtana, of the same steel and temper as Joyeuse and Durendal.
- Dialogue - Sometimes Grunts or Marines will shout "They're everywhere!", similar to the BOBs of Marathon.
- Foehammer - A level in Marathon: Infinity is called "Foe Hammer".
- Level title - Marathon has a level "If I Had a Rocket Launcher, I'd Make Somebody Pay", Halo has a part "If I Had a Super Weapon..."
- Light markers - The Covenant light markers in Two Betrayals bear a resemblance to Pfhor staffs.
- 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 which is title the "SPNKR X-18 SSM Launcher".
- Rampancy - If the player kills Captain Keyes in the first level, Cortana says, "The Master Chief has gone rampant."
- The MA5B Assault rifle is similar to the MA-75B assault rifle in terms of ammo and name
- The flamethrower in Halo PC has a similar name to the flamethrower found in Marathon : 7057 = TOZT
- The Flood resemble the Zombie Pfhor, an enemy which was cut from Marathon 2 during its development.
- The Plasma Pistol is much like the Fusion Pistol from the Marathon series, which also shares a vibrating overcharge shot.
- On the level "Pillar of Autumn," a few bulletin boards can be found near the bridge. One paper on the bulletin boards mentions a "3 Speed Manual Transmission Colony Ship" for sale, which is a reference to the Marathon level, "Colony Ship for Sale! Cheap!" as well as terminal text in Marathon, which also mentions a manual transmission colony ship.
Halo 2 Edit
- UESC - Lord Hood says, "United Earth Space Corps;" Marathon features the Unified Earth Space Council.
- Marathon cruiser- On the first cutscene of the games we can see a Marathon Class Cruiser near Cairo Station.
- The multiplayer map "Foundation" is based off of the Marathon "Thunderdome" levels.
- The multiplayer map "Gemini" is based off of the Marathon level "Duality".
- The Elite rebellion against the Covenant parallels similar events in the Marathon series. In Marathon 1, Durandal convinced a group of S'pht to rise up against the Pfhor who enslaved them; and after Durandal's disappearance in Marathon 2, 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, boi!", possibly reffering to the Marathon 2 level named "Eat it, Vid Boi!"
- There is a subchapter in The Great Journey named "Delusions and Grandeur". Marathon Infinity has a network level named "Delusions of Grandeur".
Halo 3 Edit
- On the last cutscene of the level Floodgate, when the Arbiter is bringing human weapons the weapons are the same weapons "a M7057/Defoliant Projector and a Rocket Launcher " are held in the same position as Bob's picture in Marathon Infinity,
- There is an achievement for 'accessing all the terminals in the campaign' which is called Marathon man.
- Boxes marked TRAXUS can be seen throughout the levels set on Earth. Traxus IV was the name of a famous rampant AI in Marathon's universe.
- 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.
- The way the brute holds the marine captive on Sierra 117 is possibly a reference to the L'howon chapter screen.
- A marine can be heard saying (without the IWHBYD skull) "Kill 'em all, sort 'em later", which may refer to the Marathon: Durandal level "God Will Sort the Dead". Sergeant Pete Stacker can also be heard saying "Let God Sort 'em out!", which is also a reference to the level.
- 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.
- In Halo 3, the toolboxes and small toolboxes have the word Traxus written on them, referencing the rampant AI Traxus IV.
- In Halo 3, there is an armor permutation called Security armor, which bears a striking similarity to the armor worn by the main protagonist of Marathon. It also has the Marathon logo in the helmet.
Halo 3: ODST Edit
- There is a multiplayer emblem labelled as, "Tycho". However, the emblem is actually the Pfhor insignia.
Halo 4 Edit
- The overall design of the Prometheans appear to be inspired by the S'pht. Upon 'death', the bodies of the Promethean warriors would dematerialize into data particles before completely disappearing.
- While the 'Reclaimer' glyph was altered due to legal reasons with Bungie and 343 Industries, the design still bears a large resemblance to the original Marathon symbol.
- Rampancy is a major feature of Halo 4's plot.
- Cortana Letters - These messages are riddled with references.
- Drinol - Similarity with Drinniol, a Marathon foe.
- Hunter - Similarity with Marathon foe of the same name and armor.
- Juggernaut- is the name for a Pfhor military unit and also a deleted form of the Flood.
- Marathon-class - A class of Cruisers in the Halo series
- Multyplayer - The multiplayer game "Oddball" is derived from Marathon's "Kill The Man With The Ball", which had the same objective.
- In both Halo and Marathon, there is a company called Misriah on Mars.
- A secret level in Marathon Infinity was named "Hats Off to Eight Nineteen" (after the initials of Hamish Sinclair (H=8 S=19), a dedicated fan). (Master Chief's service number and a 7 reference).
- An early promotional brochure(?) for Halo used the tagline "Somewhere in the heavens, Halo is waiting", a variation on Marathon's original tagline.Template:Fact
- Marathon 1 takes place in a ship that is orbiting Tau Ceti IV, and there is a system in Halo called the Tau Ceti system (although that star does really exist).