Gene

Gene, also known as Viper, was the commander of FOX during the San Hieronymo Takeover. Gene's unique sneaking suit color was never shown.

Early Life
Originally known under the codename of Viper, Gene joined the FOX unit after Big Boss left. In his career, he had studied political science outside of the military, as well as being a rather prominent medical doctor. In one mission when he was a FOX operative, Gene rescued Elisa/Ursula from East Germany and adopted the "twins". Some time later, Gene became the product of the "Successor Project", the goal of which was to create the "ultimate battlefield commander" modelled after The Boss.

In 1970, Gene became the FOX unit's central member and led the San Hieronymo Takeover hoping to turn the base into Army's Heaven, a new nation run for and by soldiers. Gene's 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, and exhibited 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 uses his gifted voice to release Elisa's dark and powerful second personality, Ursula, and Gene's reflexes were also faster even than Null's reflexes (This was because one of the reasons for the Successor Project was to create an Ultimate Battlefield Commander to control The Perfect Soldier, Null). Gene was also aware that Cunningham's true employers were the Pentagon and Gene was also in league with Ocelot and Major Zero in their plans of forming The Patriots, but these plans never bore any fruitation.

Big Boss confronted Gene near the end of the San Hieronymo Incident and Gene taunted him with the information from the "deviously cunning strategist" who planned Operation Snake Eater to hints about "soldier genes". Gene murdered Elisa/Ursula, exemplifying his hypocritical, two-faced nature and launched Metal Gear RAXA, resulting in a fight to the death with Big Boss. However, Big Boss managed to triumph, allowing Gene the revelation that Big Boss was indeed the true successor after all, and relinquishes the funds for Army's Heaven. His last words are reminiscent of the last words of The Boss, and he pleads with Big Boss to go find his calling.

Trivia

 * Gene referring to himself and Big Boss as "like brothers" mirrors the relationship between Solid Snake and Liquid Snake with Naked Snake/Big Boss mirroring Solid Snake and Gene mirroring Liquid Snake.
 * One of his telepathic command ability quotes during the final battle mirrors The Boss's statement to Naked Snake in their final encounter in Metal Gear Solid 3.
 * The trench coat Gene wears is nearly identical to the one worn by Big Boss in promotional art for Metal Gear Solid, the one worn by Liquid Snake in Metal Gear Solid, and the one worn by Big Boss in Metal Gear Solid 4.
 * It's possible that through the "Sucessor Project", Gene is the first Genome Soldier.
 * There have been some hints that Gene has a deep amount of respect for Big Boss, as he comments that he's impressed when he noticed that Big Boss was awake during his conversation with Cunningham, as well as instilling Null with strong emotions. Some statements during the final battle seem to imply that he also wants Big Boss to win, or at least have a challenging match against Big Boss.
 * The details of Gene's Army's Heaven, his dream Soldier Nation existing under the shadows bears several similarities to how the Patriots would emerge, giving an early clue as to what his true loyalties were. Also, Gene's Army's Heaven can (in a way) be considered a precursor to the idea of Big Boss's Outer Heaven.

Gene