Blood Knight: Some of his reactions during his fight against Big Boss indicate that he enjoys a challenging fight against Big Boss.
Charm Person: Gene's ability. Gene has a hypnotic voice and is also very good with words; he was engineered to become the "ultimate commander" which means he is very good at managing morale. Early on he uses his voice to encourage the men working on RAXA. Later he uses his powers in a much more sinister way: he convinces all his soldiers to commit suicide by telling them about an Enemy Within, and does the same to the scientists over their conscience of abusing Null, and then he says that one of the men with Snake is a traitor who's going to start killing them, driving them into a frenzy which causes them to all start shooting each other.
Compelling Voice: He manages to actually get soldiers to have their morale boost simply by talking, literally. It is stated, or at least strongly implied, that this was the result of the Successor Project.
Expy: Gene is the game's equivalent of Liquid Snake, an Evil Counterpart to the hero. But whereas Liquid was Solid Snake's literal evil twin, the relationship between Naked Snake and Gene is a bit less obvious, since he is not an actual twin, but a super-soldier trained in the image of Naked Snake's mentor, The Boss. Gene also takes his codename "Viper", from the antagonist in Metal Gear: Ghost Babel, Black Arts Viper, who was that game's equivalent of Liquid Snake.
Genius Bruiser: His bio in the Database as well as his careers in the game itself implies that he studied Political Science outside of the Military and was a prominent medical doctor. He was also shown to be a skilled strategist and capable of waging war, and capable of knowing exactly where to increase or decrease the morale of soldiers. He's also insanely fast, capable of speaking with a hypnotic voice, excels at hand to hand combat, and was implied to possess enough endurance and determination to return from the battlefield alive, a lot of these being the byproducts of his being created via the Successor Project.
Go Out with a Smile: Gene faces his death with dignity, even praising Big Boss for surpassing him and hands him the funds to build what would become Outer Heaven.
Meet the New Boss: The battle with Gene is more or less a replay of Solid Snake's first duel with Big Boss. The similarities can be seen in Gene's appearance (white hair, khaki tranchcoat), his anti-government diatribe, and various quotes during the battle ("It seems I underestimated you!").
More than Mind Control: Gene doesn't control people's minds directly so much as massage their morale. A good commander is supposed to be able to motivate his troops, after all (and the first time we see him use his Compelling Voice, it's to reassure his troops). He turns this around later when Big Boss and a bunch of Big Boss's troops assault him; he devastates their morale with a few well-chosen words to cause paranoia among them and with a single shot causes them to all start shooting each other.
Nietzsche Wannabe: Gene expressed a belief that humanity is good for nothing except being "violent, foolish, fragile creatures" and fighting amongst each other when forcing them into a mass suicide riot.
Pet the Dog: It's somewhat implied that the reason why he went as far as to generate mental shielding powerful enough to prevent even Ursula from reading his mind in order to avoid her betraying him is because he didn't wish to have to kill her as a result. Basically, due to his skills, he wouldn't have to worry too much about being harmed in any way by Ursula should she betray him, as he proved by stabbing her with his speed, knowing that even though she could predict his movements, she won't be able to evade his speed.
Spanner in the Works: Ocelot's conversation with the mysterious man (later revealed to be Zero) in The Stinger implied that Gene was supposed to simply point the ICBMG at Washington DC, and not actually fire the ICBMG. Unfortunately, he did exactly that, although they apparently anticipated the likelihood and had Naked Snake defeating him as their insurance policy.
Well-Intentioned Extremist: He wanted to get rid of the Philosophers and free the world from their control, although his method of doing so was launching a WMD at Virgina, USA and then making it seem as though the Russians did it. He also seems to believe that having the masses essentially pour their life energies and be sapped of their free will and commit sacrifice was something The Boss would have wanted.
A Red Army soldier during the San Hieronymo Takeover. He was the first person recruited by Big Boss and Roy Campbell in Portable Ops.
Brainwashed: Subverted: Jonathan is initially suspected of being brainwashed by FOX when Jonathan laughs at Roy and Snake's statements on wanting to help the Ex-Soviet Personnel be free of FOX's control over them, but he then denies it, and explains the real reason why they are serving FOX.
Combat Pragmatist: After Jonathan is kidnapped by Big Boss with the intention of recruiting him into their resistance, Jonathan, upon regaining consciousness, attempted to attack Snake, only for his punch to be blocked by him. He then restrained Roy Campbell and stole his gun and attempted to use it on Big Boss to escape, only to end up flattened on the truckbed by Big Boss's CQC skills. Unlike most examples of Combat Pragmatism, Big Boss actually compliments Jonathan on it ("Quick thinker, too. They've trained you well. You're a good soldier.").
Flat Character: While technically a unique character, he only exists to show off how the recruiting process works by being the first enemy solder who can be captured by Snake. From that point onward, he gets no real character development (his name is not even mentioned outside his status screen) until he is killed off during a cutscene.
Heel-Face Turn: Sort of. He joins Snake and Campbell early in the game.
Mistreatment-Induced Betrayal: The reason he was initially working for Gene is out of disgust for his and the other Soviet personnel's treatment by the Soviet government. To put it bluntly, the soldiers and other personnel had to put up with the unbearable climate of San Hieronymo, with poor food supplies, and several of their comrades dying either from disease or from aiding in battle against the Colombian regime at the time, all because they wanted the Soviet Union to prosper and win the Cold War in their favor. However, come 1970 and Detente, the Soviet Government "repaid" their efforts by marooning them on the peninsula, cutting off all supplies and communications, all to make it seem as though he and his soldiers were Renegade Russians in case the incomplete base was ever discovered by the United States and its proxies.
It's even more powerful than it seems since he does this immediately after Gene claims humanity to be "fragile, foolish, violent creatures" and telling Big Boss to see for himself humanity's true nature. In a way, his sacrifice is the ultimate contradiction in Gene's philosophy.
Vodka Drunkenski: An optional radio call to Para-Medic (should she be recruited) via Jonathan, any of the Soviet personnel, or, heck, any character who isn't Naked Snake, will strongly imply he and the other Soviet soldiers recruited are of this trope. It's probably justified, as they had been marooned by the Soviet government for no reason other than to have a convenient excuse about why there is a missile base in Colombia made by the Soviets when they are doing the SALT talks.
An old war buddy of Snake during the Vietnam War. He received a severe injury which cost him the ability to regulate his body temperature to the point that his body would burn up and was assumed dead by Snake, but his body was recovered by the U.S. government who put him through surgery and gave him a suit filled with liquid nitrogen. He was then trained by the CIA to be an "Anti-Snake" soldier. He was present at the San Hieronymo takeover where Cunningham assigned him to lead the search for Snake and Roy Campbell.
Anti-Villain: It's fairly clear that the only reason he agreed to partake in Gene's rebellion was so he could redeem himself for his actions as the Anti-Snake.
An Ice Person: Due to injuries suffered in Vietnam and the resultant cooling suit he was hooked up to keep him alive.
Berserk Button: Apparently being called a "monster" by someone, especially if that someone also attempted to kill him first, is something he does not like.
Death Seeker / I Cannot Self-Terminate: It is pretty clear that he is also willing to accept his death as he felt he was irredeemable for basically having to participate in Wetworks as part of being an "Anti-Snake" soldier, something that's made very clear that he did not enjoy at all, if he couldn't beat Big Boss at all.
Flashback Nightmare: Python states that he got stuck with them due to his Wetworks missions, when explaining what he had done with implied guilt for what he has done.
A young woman with psychic abilities who follows Gene in his rebellion. However, she decides to help Snake when they meet, giving him drugs to cure Campbell's malaria, and warning him about her sister, Ursula. It turns out that she is Ursula, and is a split personality.
Child Soldier: The characters note multiple times that she's significantly young to be a soldier, or a medic, for that matter.
Disney Death: She appears to die when RAXA is destroyed, but shows up later where she destroys the ICBMG activation control panel with her psychic powers. However, Gene kills her immediately afterwards.
Flashback Nightmare: She states that the Kyshtym Disaster in the Ural Mountains, her parents deaths, and her being irradiated still haunted her in her dreams.
Heel-Face Turn: She technically does it twice, once with each personality.
The FOX unit's interrogation specialist. He joins Gene's rebellion. He turns out to be working for the Pentagon, and his role was to force Gene to launch a nuclear strike at the Soviet Union, destroying the reputation of the CIA, and then destroy the base using a Davy Crockett to remove all the evidence.
Alas, Poor Villain: In-universe, Gene expresses pity on Cunningham for dying before he could ever realize that he was simply a pawn.
Black Dude Dies First: Kind of: He'll be either the first or the second renegade FOX member to die (not counting Elisa/Ursula, who had survived their duel with Naked Snake), depending on the player's decision on how to defeat Python.
A Red Army colonel. He was in command of the San Heironymo Peninsula, but after Gene's rebellion his men turned on him and he was forced to go in to hiding.
Chekhov's Gunman: He first appears relatively early, where he is seen encountering Python and is locked in a cell and Snake shoots the lock, freeing him. Later, he takes control of Metal Gear RAXA, and unleashes it against Gene and his followers. He is killed by Ursula after that.
Vodka Drunkenski: He is the (former) Soviet commander of the San Hieronymo missile base, and he is strongly implied to be drunk when Snake first encounters him. Probably justified, as not only is he literally marooned on a desolate peninsula with no contact, but most if not all of his soldiers had also deserted him thanks to Gene.