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All throughout the Phantom Pain Incident, Pequod personally assisted Venom Snake by deploying him out to certain locations present in Afghanistan and the Angola-Zaire border region via chopper to get him to his mission areas, as well as flying him to Mother Base at certain intervals and providing additional air-support.
One Pequod pilot was killed by the Parasite Unit's metallic archaea while transporting Venom Snake and Code Talker out of the Angola-Zaire border region. The chopper's windshield was shattered, causing glass to fly into his face and mangle it beyond recognition.
Another Pequod pilot was guided by Quiet to the mortally injured Venom Snake's location via iDroid during a brutal sandstorm, saving Snake's life and expressing surprise and cheer upon discovering the supposedly mute Quiet was the one guiding him all along.
Behind the scenes
Pequod follows the trend of Moby-Dick-based codenames in Metal Gear Solid V: The Phantom Pain. In the novel, the Pequod was the title of the ship commandeered by Captain Ahab in his quest for revenge on the white whale - at the Dhekelia SBA Memorial Hospital, Venom Snake was labeled "Ahab", paralleling his own fight for vengeance. Other examples of Moby-Dick in The Phantom Pain include Big Boss being known as "Ishmael" while at the same hospital, and a chopper pilot present at Diamond Dogs' attack on OKB Zero being designated "Queequeg."