WMG / Marathon

The events of Marathon is all a dream.

That's why Infinity's chapters are titled Despair, Rage, and Envy, and the final level being Aye Mak Sicur.

Infinity's ending shown the Security Officer's acceptance

Mixing this in with Durandal's optimistic ideals of humanity, all the torn bone and flesh hosted by machine were Dissected, and all that was left are strands of artificial muscle and skin tissue still necessary. The apparent disfigurement in his fingers are damage from an explosion.

The Security Officer will return in Destiny, which is a distant sequel to Marathon

Don't forget that "Destiny" was the name Durandal gave the officer as the universe closed. Or those leaked documents that claimed Bungie was working on a Marathon sequel. And perhaps the Traveler is Durandal in his Jjaro dreadnought.

Marathon and System Shock exist in the same universe.

The first cases of Rampancy appeared in the 21st century, according to a log file in the first game. It could be highly possible that the first case—or one of the first and most well-known cases—of Rampancy resulted in SHODAN's massacre of Citadel Station in 2072.Another factor in this is that the crashed grove where SHODAN's backup and what would later become The Many were on Tau Ceti V, one planet off from the colony that the Marathon was headed to.

The Security Officer is the descendant/reincarnation of The Sergeant.

The unformatted terminal in "Kill Your Television" alludes to reincarnation and may have been written from the SO's point of view. That "old dream" that the SO is reminded of as he prepares to board the Marathon might be faint memories of entering the anomalous pyramid.

Durandal tried to save Tau Ceti IV.

Early in the second game, he tells the Security Officer about the colony's fate, and decided against leaving the BoBs on his captured ship down there when he realized that the colony was about to be lost. He also sounds somewhat remorseful about the whole thing (note how he claims direct responsibility for it all, and immediately tries to justify his actions as better for humanity in the long run than if the Pfhor had continued on to Sol). Durandal actively tried to fend off the Pfhor and save the colony—unfortunately, he had neither enough naval combat experience nor numbers to succeed.

The Security Officer was actually manipulating everyone during the events of Infinity

By pretending to be manipulated, he was able to push himself towards his goal: Stopping the W’rkncacnter

The Security Officer retains the consciousness of Traxus IV, the first AI to go Rampant

This was actually suggested by Greg Kirkpatrick in an informal Reddit AMA as a possible reading of the dream levels, so this one may actually be semi-canon. Though it's also possible he was just pulling our legs.

The Security Officer is a Time Lord.

...How has no one gotten put this here yet? Actually, the Jjaro are all Time Lords. It's why they're so resistant to anything changing in Eternal. The Security Officer is what would've happened if the Doctor hadn't developed such an antipathy to guns. If we're not just going with "the Cybernetic Junction is his TARDIS", then Leela probably behaves most like the TARDIS in "The Doctor's Wife". Durandal is River Song, of course; they're both a bit psychotic and a bit possessive. Hathor is the Master.

The Security Officer is actually a Servant, and Durandal is his Master

(WMG for mods goes on the WMG.Marathon Expanded Universe page.)