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 (Level).
On the Spartan Insignia, there is a gold Marathon logo.
The control panels on the elevators, on the level The Covenant (Level), 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 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.Zombie Pfhor Image
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.
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".
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 can be dual-wielded.
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.
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 Halo 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.
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).