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 acceptanceMixing 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 MarathonDon'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.