As the Halo 2 connection has been clearly demonstrated, HA is already at least indirectly connected to Marathon (HA->Halo2->Bungie->Marathon). However, there has been some speculation that the connection is deeper. The entity that "hacked" TheIlovebeesCom seems to be more circuits than cells, leading to my belief that it is an AI.
From gspawn: I dug up a quote from [WWW]here

Q. Is Marathon the prequel to Halo? A. No, Marathon is a separate story, with wholly different characters, story and gameplay.

Also, to further their point: Q. Are the Pfhor related to The Covenant? A. No, although they do share some traits –such as enslaving client races, they are entirely separate and each exists in a different "universe."

And: Q. Is it true the rocket launcher in Marathon is the same as that in Halo? A. Nope, but they both use the expression "SPNKR." It's a rocket thing.

Bungie has said several times now that, although there are LOTS of (intentional) similarities between Halo and Marathon, the two universes are entirely seperate (at least for now). Take all these connections with a grain of Bungie brand salt.

[WWW]Marathon, Marathon 2 and Marathon Infinity were three first person shooters by Bungie, makers of Halo. The basic story of Marathon is that of a Mjolnir Mk IV cyborg defending the Tau Ceti colony, and later its survivors, against a slaver race known as the Pfhor. Integral to the story are the three Marathon AIs - Durandal, Leela, and Tycho. The player receives instructions from computer term(inal)s, but the point behind those instructions, depending on the AI giving them, is often different.

Early in the series, it becomes obvious that Durandal, the AI designed simply to open and close the Marathon's doors, has become [WWW]rampant, and his messages become more [WWW]arrogant and [WWW]childish {Terminal 3}.

Rampancy has been mentioned in Halo (Cortana claims the Master Chief has "Gone Rampant" if he shoots his captain early in the series. Also, Cortana acts Rampant the moment she is inserted into Halo's computer systems, with her eyes glowing red and an arrogant tone afterwards.

Others have noted [WWW]similarities between the known situation and what happened to the Marathon AI 'Leela'.. The Operator's behavior is [WWW]reasonably consistent with that of an AI in the early stages of [WWW]rampancy. Discussion on rampancy in [WWW]this thread. And then there's that whole [WWW]sevens thing. Finally, another name for Durandel, the sword in the Song of Roland. is Durandal. The most famous rampant AI from the Marathon is named Durandal. Coincidentally, Dana is the webmaster of

A good synopsis of the Marathon story can be found on [WWW]

[Quick note: ToBI link has been found to be some overzealous forumgoers. Disregard.]