CIA Director

The Director of Central Intelligence (referred to colloquially as the DCI, CIA Director, or simply Mr. Director) was in command of the CIA from the end of Operation Snake Eater until the San Hieronymo Takeover.

Biography
Shortly after Operation Snake Eater, the CIA (the American Philosophers) brought in the DCI was to replace the previous DCI who originally planned and orchestrated the operation. Although this was supposed to secure the CIA against inside threats, the DCI nonetheless used the operation as an opportunity to secure the Philosophers' Legacy for himself with the intention of reviving the American Philosophers.

After Naked Snake was awarded the "Big Boss" codename by President Lyndon B. Johnson following the success of Operation Snake Eater, the DCI attempted to shake Snake's hand. Snake intentionally ignored the gesture and departed, upset by the truth behind the operation. Immediately after this insult, a senior DOD Official spoke with the DCI about the possibility of creating an infiltration unit like FOX within the Army to handle their top-secret sneaking missions.

The DCI later received a call from ADAM about the outcome of the mission, along with Aleksandr Leonovitch Granin's blueprints that he had acquired. Their conversation revealed that the DCI had only acquired half of the Legacy. It was assumed that the KGB (the Russian Philosophers) possessed the other half.

In 1970, the DCI instigated the San Hieronymo Takeover by ordering the FOX unit (under Gene's command) to "steal" a nuclear missile from a convoy and pretend to defect to the Soviet Union. By handing over Metal Gear to the Red Army, the Cold War would be prolonged, thus maintaining the CIA's power and influence. When he believed the missile was heading towards America, based on trajectory data supplied by Major Zero, he (along with two bodyguards) retreated to an underground bunker where he was confronted by Ocelot (ADAM), who had managed to sneak down to the bunker easily due to the FOX unit not being around. After revealing that he had "documents" on the Philosophers (which included the identities of the Philosophers' members) in the event of a nuclear aftermath, Ocelot killed the two bodyguards and the DCI after the events on San Hieronymo, although not before declaring that he intends to end the Philosophers and create "a world that she envisioned." Ocelot staged the death of the DCI to appear as a suicide, allegedly because he felt responsible for the missile being launched.

Posthumous
During the events of the Peace Walker Incident, Big Boss, when attempting to Chairman of the Joint Chiefs to stop the launch of nukes and explaining that the missile data they received was actually fake, referenced when he refused to shake the CIA Director's hand, citing that he refused because he "knew where his loyalty lied."

Behind the scenes
The CIA Director first appears in Metal Gear Solid 3: Snake Eater, voiced in English by Paul Collins. However, he has no actual dialogue in the game, only making a minor sound of disgust after Naked Snake refuses to shake his hand. The DCI is modeled after the real-life Cold War era director John McCone, but isn't directly named. The historical McCone died in 1991 of natural causes. Likewise, in the director's commentary for Metal Gear Solid 3, Kojima implied that he was originally intended to be McCone.

The CIA Director was originally intended to have given Snake the Distinguished Service Cross and the Big Boss codename, following Operation Snake Eater, though this was changed to President Johnson in the final game. According to the Metal Gear Solid 4 Database, the DCI had apparently informed the U.S. Government that they had failed to retrieve the Philosophers' Legacy, following Operation Snake Eater, and had instead kept it for himself.

The DCI later appears in Metal Gear Solid: Portable Ops, voiced in English by Jesse Corti. He was suspected to be the "deviously cunning strategist" that Gene alluded to, since he was originally intended to have been responsible for planning Operation Snake Eater in Metal Gear Solid 3 as well as Ocelot's statements shortly before executing him. However, this was retconned in Metal Gear Solid: Peace Walker when Hot Coldman was revealed to be the mastermind behind the mission. Likewise, it was originally implied in the ending of Metal Gear Solid 3 that the CIA Director was the one who founded the Patriots, due to both the ending timeline mentioning that the other half of the legacy was recovered by 1971 and used to form the Patriots as a revived version of the American faction of the Philosophers and Ocelot's ending phone call telling the DCI that they are getting closer to reviving the American faction. However, this was retconned in Portable Ops with the DCI's death at Ocelot's hand as well as the involvement of the "Man with the same codename as Null" making it unlikely, as well as in Metal Gear Solid 4, which revealed that Zero was actually the founder of the Patriots.

The DCI stars in Metal Gear Solid 3: Subsistence 's Secret Theater, more specifically in the film Payback where he humiliates Snake by defeating him with CQC. He did this out of revenge for Snake not shaking his hand after Operation Snake Eater. He then makes another attempt to shake Snake's hand which Snake accepts. After shaking hands, they end up dancing and kissing. In the end, the title of the film changes to "Metal Gear Stupid."