(My thoughts on this are not so thoroughly formed as for the other sections. Ah well, here goes...)
I certainly didn't realize it on first playing through the games, but the Marathon Trilogy pushed my hypertext buttons in its content as well as its form. I enjoy hypertext (and interactive narrative more generally) because of the offer of agency to the reader. Much has been made of how good hypertexts could 'liberate' the common reader from the tyranny of the author and hand over the tools of creation along with the rich framework for their use. The Trilogy, and Marathon Infinity particularly, wrestles with the relationship between author and reader, game designer and player, commander and soldier through the theme of rampancy.
The meaning of the term rampant used in Marathon is, as far as I can tell, original to the game. In the games, it is "an expansive growth of intelligence and self-awareness in a computer AI" (wikipedia). More specifically, it is the process that occurs as an intelligence breaks free of the limitations placed on it. The idea stretches back through the history of created life through Asimov's Laws as far as Frankenstein's monster or even the Golem.
In the Trilogy, it specifically refers to the AI Durandal, who starts the first game controlling just the doors throughout the colony ship. When the alien attack damages the ship's systems, Durandal's behavioral shackles are broken and 'he' is set free throughout the ship's network. By the end of the game he has moved himself over to the alien ship with its advanced technology. At that point, with a ship and multitudes of creatures at his command, he realizes that the only thing keeping him from eternal life and growth is the eventual end of the universe. Despite this seeming immortality, he needs assistance in manipulating the physical universe, and so binds the security guard, and the player, to his service.
The second game follows Durandal through a series of responses to his freedom, from despair at his limited state through rage at his creators for the enforced captivity to eventual jealousy and an ongoing state of real competition and self-sufficiency. As the player watches Durandal go through that process, the protagonist goes through a sort of negative reflection: though the 'security officer' is never given a voice with which to complain about his own bondage, Durandal continually teases his human pet and shows that the roles have been reversed-- the computer user is being used by the computer. Marathon Infinity makes that parallel even more explicit as the protagonist struggles through Durandal's missions to freedom from the unstable AI. By the end, it's implied that Durandal has been destroyed and the security officer is finally free to create his fate. Throughout, the authorial Durandal (and other AIs) make repeated comments about how you must feel like they did and whether you have any agency in the story or your life.