Gene

Overview
Formerly known under his FOX codename of Viper, Gene assumed control of the FOX after Naked Snake's departure from the unit. He was the one who led the unit's revolt in the hope of realising his vision of The Boss' wishes, Army's Heaven. Gene believed he was the only one capable of fulfilling The Boss' wishes due to him being a result of the “Successor Project”, a project designed to synthesize the "Ultimate Battlefield Commander" whom was to be modelled  after The Boss herself. 
He was also initially planned to be included in Major Zero's plans to found The Patriots, his death however cut him out of the picture.

Gene has superhuman reflexes and his voice holds a manipulative mind-altering trait. This, combined with his history in Political Science, allowed Gene to make speeches which he used to coerce loyalty and trust in his soldiers. Gene also uses his voice to unlock Elisa's darker personality: Ursula.

San Heiroynmo
During their final confrontation, Gene taunted Snake with information of The Boss's defection as well as other things such as corruption within the White House and  genetic engineering. Gene murdered Elisa, exemplifying his hypocritical, two-faced nature and launched Metal Gear RAXA. Gene and Snake then fought to the death, with Big Boss as the victor, causing Gene to realise that Big Boss was  the true successor after all. He then gives Big Boss the funds for Army's Heaven (later Outer 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

• Big Boss and Gene's rivalry mirrors that of Solid Snake and Liquid's, a "brother" fighting to prove their superiority.
• Gene always has a Bowie Knife in his inventory, when equipped it can be used as a normal knife or if in first person mode he can throw a trio of daggers.
• Gene is the first known person to be seen wearing the trench coat which Big Boss later used as the trademark outwear of FOXHOUND.
• Gene's unique FOX sneaking suit is never shown as he never removes his coat.
• Many of Gene's lines and speeches bear heavy resemblance to The Boss' words to Snake during Operation Snake Eater.