Gene

Gene, also known as Viper, was the commander of the CIA special forces unit FOX, during the San Hieronymo Takeover.

Early Life and Career
Gene joined the FOX unit after Big Boss (Naked Snake) had left, receiving the codename Viper. He subverted Major Zero's authority and established his own. In his career, he had studied political science outside of the military, as well as being a rather prominent medical doctor. In one FOX mission, Gene/Viper rescued Sokolov from Russia and reunited him with his family. During one mission as a FOX operative, Gene rescued Elisa and Ursula from East Germany and adopted the "twins". It is understood that he served as their mentor; teaching Elisa her skills in medicine and chemistry while training Ursula as a soldier. Some time later, Gene underwent experimentation on the "Successor Project", the goal to create the "ultimate battlefield commander", modelled after The Boss. As a result, he was given superhuman abilities. During this time, Gene developed "CQC Enhancer", an enhanced version of CQC with destructive power well beyond Big Boss's CQC and changes in the composition of techniques. At some point after Operation Snake Eater, he came across the identity of the man who was behind The Boss's death.

In 1970, Gene became the FOX unit's central member and led the San Hieronymo Takeover. Gene, along with Ursula, accompanied Cunningham when they searched the area for escaped prisoners (Big Boss and Roy Campbell) aboard a Hind-A gunship. Afterwards, they arrived at the Research Lab, where Ursula and Gene both successfully predicted that portions of a scaffolding were about to collapse, and warning Cunningham to remain still. Afterwards, when a soldier apologized for the accident, he forgave the soldier, and then demonstrated his hypnotic speech ability to the rest of the gathered soldiers. He himself apologized for making the work seem more important than the soldiers' well-being, and promised that the days when soldiers were used as political tools would be ended.

After Big Boss was again captured, Gene remarked that intel extracted by physical torture is unreliable, and questioned Cunningham's abilities as an interrogation specialist. When Cunningham suggested that he use truth serum, he mentioned that it wasn't reliable since Big Boss was a former FOX agent. He ultimately let Cunningham prepare the truth serum, but under the condition that he would speak to Big Boss first. He explained to Big Boss, who was awake throughout the whole conversation, that the entire "rebellion" was actually staged by the CIA in order to prolong the Cold War.

Shortly thereafter, Gene had a telephone conversation with his "new world" with his conspirator Ocelot. After the call, Gene stopped a rampaging Null using his inhumanly fast reflexes and ESP abilities.

Big Boss was eventually rescued by his allies and Elisa was taken with them. Gene anticipated that Big Boss and his group would learn from Elisa where the ICBMG was located and would try to destroy it. He then secretly replaced the ICBMG with Metal Gear RAXA at the Plant. As Big Boss infiltrated the facility, Gene arrived with a large platoon of his soldiers, accompanied by Hind A helicopters, in order to apprehend him. However, an event that not even Gene anticipated occurred, in which Colonel Skowronski hijacked RAXA. Gene then unleashed his true trump card, awakening Ursula, who was actually the twin personality of Elisa. Gene had Ursula commandeer RAXA using her powerful psychokinesis, and giving it abilities far beyond its potential. While RAXA was ultimately destroyed, the battle still bought more than enough time for Gene's men to finish loading the real ICBMG with nuclear weapons and transport it out of the Plant to the Missile Silo. Gene then gave another one of his speeches, only this time it is far more threatening in nature, forcing both his men and Snake's battalion to go into a mass riot that resulted in many casualties, including the death of Jonathan. Gene then left for the Missile Silo.

Big Boss eventually confronted Gene, where the latter revealed that not only was he aware that Cunningham was trying to betray him, but he was actually planning to launch Metal Gear into Virginia, USA, instead of Russia as previously believed. He then taunted Big Boss with the information regarding the "deviously cunning strategist" who planned Operation Snake Eater, and revealed he was hoping to turn San Hieronymo into Army's Heaven (a new nation run for and by soldiers), and hinting about "soldier genes". Elisa/Ursula, revealing her survival of RAXA's destruction, destroyed the launch panel and attempted to stop his plans. However, Gene, with his much quicker physical abilities, murdered her, exemplifying his hypocritical, two-faced nature and proceeds to launch the ICBMG via a backup launch control room. This resulted in a fight to the death with Big Boss to determine who the true successor of The Boss was. However, Big Boss managed to triumph, allowing Gene the revelation that Big Boss was indeed the true successor after all, and relinquishing the funds and resources for Army's Heaven. His last words were reminiscent of the last words of The Boss, and he pled with Big Boss to go find his calling.

It was later revealed that Ocelot and his other conspirator (whom Gene earlier referred to as "the man with the same codename as Null") had actually intended for Gene to only point the ICBMG towards Langley to lure the CIA Director with "documents" about The Philosophers over to Ocelot. However, they were unaware that Gene was serious in launching the ICBMG.

Personality and Abilities
Gene's intense charisma gave him the power to win people's hearts and minds. His voice was given a special manipulative mind-altering power where he feigned loyalty and strength to those who followed him but secretly despised the human race in general, exhibiting qualities of deeply pathological, tyrannical behavior. During Gene's speech-making, he could swell up loyalty and powerful, trusting emotions in his soldiers, but also used it to instill fear in mobs and cause riots to break out, laughing cruelly as he did so. Gene also used his gifted voice to release Elisa's dark and powerful second personality, Ursula.

Genes reflexes were said to be even faster than the Perfect Soldier Null, due to being a product of the Successor Project, along with his abilities of ESP. He also seemed to possess some limited telekinesis that gave him the power to defeat Null with a single direct mental blast. Furthermore, Gene was also a master of "Zero Shift", an ability much like teleportation, which allowed him to kill Elisa/Ursula before she had a chance to react. He also used this ability during his battle with Naked Snake, though employing the technique too often left him physically exhausted, giving Snake an opening in which to defeat him.

Trivia

 * Gene's reference to himself and Big Boss as "like brothers" mirrors the relationship between Solid Snake and Liquid Snake.
 * Gene's unique Sneaking Suit color within FOX was unknown.
 * The trench coat that Gene wore is almost identical to the one worn by Big Boss in his later years, and also those worn by the renegade FOXHOUND members during the Shadow Moses Incident.
 * One of Gene's telepathic command quotes during his final battle with Big Boss mirrored The Boss's statement to Naked Snake in their encounter at Dremuchij North during Operation Snake Eater.
 * There were hints that Gene had a deep amount of respect for Big Boss, as he was impressed by the fact that Big Boss managed to remain conscious after enduring Cunningham's torture, as well as instilling Null with strong emotions. Some statements during the final battle seemed to imply that he also wanted to have a challenging fight against Big Boss.
 * The details of Gene's Army's Heaven existing in the shadows, bears several similarities to how The Patriots would emerge, giving an early clue as to what his true loyalties were. Also, Army's Heaven could (in a way) be considered a precursor to the idea of Big Boss's Outer Heaven.

Behind the Scenes

 * Gene's "Zero Shift" ability is a reference to Zone of the Enders, another game directed by Hideo Kojima.
 * It is possible that through the "Successor Project", Gene was a predecessor to the Genome Soldiers and Les Enfants Terribles. On a slightly related note, Gene's English voice actor (Steven Blum) also voiced some of the Genome Soldiers in Metal Gear Solid: The Twin Snakes.
 * To unlock Gene outside of a password, the player needs to not only defeat him non-lethally, but also recruit over 200 soldiers within the same playthrough. In the EU version of the game, the way to unlock Gene is to complete Boss Rush.