The All Concealing I: The series has an odd variation of this - you play a character that is treated like a tool by most other main characters, and as such the only dialogue you get is overheard conversations in which you aren't mentioned or someone talking to you giving you orders. Aside from a short, vague prologue in each manual there is no background for your character, and he is never heard. Plenty of hints are in the game, with mentions of military cyborgs and soldiers made from the reanimated dead, but arguments still go on as to what exactly he is.
Heroic BSOD/Sanity Slippage: As shown in the dream levels terminals, the whole of Infinity is just one long look at the main character's slow breakdown. Lampshaded as well by the chapter names - "Despair," "Rage," and "Envy" are synonyms for the stages of Rampancy, "Melancholia," "Anger," and "Jealousy."
Heroic Mime: The main character at first seems like this, but in the manual and the Marathon comic, he speaks. Although one could argue that these are not canon because of how inconsistent they are, we see our little hero conversing with some BOBs in the “Simulacrums” chapter screen.
Human Pet: One interpretation of his relationship with Durandal.
Storyline-wise, the Security Officer is not the only one defending the UESC Marathon and Tau Ceti, and he does not single-handily crush the whole Pfhor invasion as much as he does some critical surgical strikes (with the help of Durandal), and letting the S'pht rebellion do the rest of the job, all while the game occasionally drops hints about the Mjolnir Cyborgs. But gameplay-wise apart from the security drones and the two Mission Control AIs you were on your own.
In the second game the formerly docile BoBs all take up arms in a much larger war (which our heroes nearly lose halfway through the game despite their best efforts), in which the Security Officer (whose One-Man Army status is more fleshed out, even if it is still vague on details) is only a small part of (albeit a very important part).
We Do the Impossible: Does this in Marathon, has a reputation for it in Durandal, and becomes somewhat literal in Infinity.
When All You Have Is a Hammer: As a security officer on the UESC Marathon, all you could do is kill the Pfhor by the thousands. It gets lampshaded in the sequels, where the AIs sometimes just tell to do what you do best.
Bad Boss: The Tau Ceti survivors consider him to be this.
Big Bad: Remember, he set things in motion for the first game, and even him helping you halfway through was ultimately part of his schemes.
On the other hand, his actions eventually result in humanity beating the Pfhor and freeing their slaves. Afterward he doesn't bother with humanity ever again (except that one time he buzzed Earth for the lulz). While he's certainly the central antagonist and incredibly selfish in his motives, whether he can be considered Bad is open to interpretation.
Break the Haughty: Durandal, upon his defeat at the beginning of Infinity, loses his massive ego, and instead of working to save himself, he gives you instructions to save yourself and leave him to die. This is also shown later in the game with a dying Durandal helping you without snarking, even though you're on his enemy's side.
Deadpan Snarker: Durandal would rather make puns at you or write songs about himself than tell you where to go next.
Do Not Go Gentle: Durandal taking out half of the Pfhor's best of the best fleet with just one ship.
Durandal: Battle has been joined in orbit and Boomer is taking heavy damage. I cannot hold out for long, but the Pfhor will not soon forget the day that a lone corvette obliterated half of Battle Group Seven, Western Arm.
Gambit Roulette: Escape from the primitive humans by locating and calling to a race of tyrannical slavers to hijack their ship with the assistance of their pet cyborgs? Beat your Evil Twin by letting him kill you, allowing your remains to be examined by his masters and taking over their ship? Use your faked death to trick a Precursor AI into following your plans to the letter? All in a day's work for rampant AI Durandal. The best part? The player eventually outdoes him. Sorta.
We Have Reserves: A big part of the reason the BoBs consider Durandal a Bad Boss in Marathon 2 is because of how cavalier he is about spending their lives.
Spaceship Girl: In charge of most important parts of UESC Marathon. Ends up being a 15-world network girl.
Team Mom: Of the three AIs, she is the one who is in general command of UESC Marathon.
Undying Loyalty: A trait mentioned in passing in the first game by Durandal, which is expended upon in the fan scenarios.
What Happened to the Mouse?: In Marathon 2, the player learns that Leela was dismantled off the UESC Marathon and sent to the Pfhor homeworld. The ending screen informs us that she didn't get to the Pfhor homeworld, having been stolen, installed in an alien race's computer system, and went very Rampant. A secret terminal hints that you might be tasked with saving her ("Captured and partially-disassembled human-coded AI trapped on alien homeworld seeks succor from a tall, dark and handsome cyborg with big guns."), but you never do.
Women in Refrigerators: Gets dismantled alongside Tycho. The final screen of Marathon 2 somewhat abruptly states that Leela still exists ten thousand years later as a Rampant AI, and the Vylae have accepted that they will never be able to expunge her from their fifteen-world network.
Back from the Dead: He was critically disabled during the initial Pfhor assault on the Marathon due the EMP blast they opened their attack with. The other ship AIs fared somewhat better, but Tycho was given up as destroyed. When the Pfhor returned in force after the game, they went over Tycho's core for reverse engineering purposes and painstakingly rebuilt him. He was not the same afterward.
Disproportionate Retribution: In Infinity the Security Officer wakes up from stasis a little earlier than predicted and Tycho asks the Officer to remind him later to kill the Pfhor Scientist for the slight miscalculation.
Face-Heel Turn: In his few appearances in the first game he was at least Anti-Durandal only, but by the time the sequel comes he really wants to kill Durandal no matter what.
Stupid Neutral: Due to his desire to maintain the balance of power, he changes alliance and begins aiding the Pfhor when Durandal makes it plain that he's not dead after all. Of course, it's too little too late.
Attack Drone/Mecha-Mooks: Marathon Automated Defense Drones, or simply MADDs, assist you in defending UESC Marathon as soon as you reactivate the defense system. Beware of the grenade launching low-flying ones, though.
Durandal: By Pfhor standards, Earth is a poorly defended low technology world, populated by billions of potential slaves.
The Leader: Robert Blake for the Tau Ceti Survivors.
Red Shirt Army: The BOBs when they are on your side; they occasionally avert it when they are positioned in such way that the Pfhor can only come from the chokepoint and at the distance, who then get slaughtered by sniper pistols, as seen in Durandal level My own private Thermopylae. In times when they are your enemies, they are quite accurate with those magnums. Notably, the way the physics models are set up in the game's data means that their strength does not vary with the difficulty setting even when they are your enemies (most likely an oversight on the part of the developers, as the option to make their strength vary was certainly there), which means that on low difficulty settings the levels where you fight them seem much more difficult than the surrounding levels, and may be part of the reason the third game has such a reputation for difficulty. The same levels may not seem particularly easier on high difficulty settings because they're pretty difficult anyway.
Vulnerable Civilians: The BoBs in the first game, where they are practically situated for maximum crossfire potential.
Hive Mind: The S'pht have a unified racial consciousness, which is why the Pfhor used brainwashing to control them instead of rule by fear (or just nuke them if that fails) since the necessary "infrastructure" was already there.
Hive Caste System: The Pfhor are hinted to be like this. In Infinity, Tycho says “bugs are so obedient” in reference to the Pfhor under his command, and they have a clear caste system in which the lower ranking members (Aggregate rank) are considered more expendable than the upper ranking ones (Willful rank).
Nuke 'Em: Nuclear bombs are the Pfhor's preferred weapon, but when THAT doesn't work?
Obstructive Bureaucrat/Vast Bureaucracy: The Pfhor empire are shown to be this here and there, enough for Tycho to almost cleanly commit casual treason by convincingly issuing orders to terminate the higher ranks of the ship he is currently on. The Game ModTempus Irae had a field day with this, with an interlude that was basically a one big "If you had to kill a superior officer and had a really good reason for it, press one" joke.
Organic Technology: The Pfhor make extensive use of this, most clearly seen in their weapons, the Hunter armor, the Juggernaut, and their Space Jockey/Alien Hive like spacecraft interiors.
Praetorian Guard: Tycho pits you against Admiral Tfear's personal guard in Infinity level You think you're Big Time? You gonna Die Big Time!. They consist of pairs of Elite gray-armoured fighters, troopers, hunters and one brown Juggernaut. And they are all mean.
Vestigial Empire: At least according to Durandal, who states that the Pfhor empire is in slow decline since the Drinniol slave rebellion.
We Will Use Manual Labor in the Future: The Pfhor are slavers who use and sell other races for various tasks, though the S'pht's application to computer engineering makes a bit more sense than usual since they're cyborgs.
Zerg Rush: The number of Pfhor you fight, especially the fighters, tend to get very high after about halfway into the games.