Shortly after Venom Snake had retrieved several child soldiers in both Africa and Afghanistan after they had escaped Mother Base, Eli, anticipating the possibility that he would get caught, had several of his child soldiers hijack a UTH-66 Blackfoot. He then, during an interrogation session, had Tretij Rebenok interfere and use Metal Gear Sahelanthropus (which was made operational again thanks to Huey Emmerich secretly repairing it with Eli and the other child soldiers help). Venom Snake and Ocelot then ran out just in time to see the chopper flying away, with Etepe pointing a rifle to the chopper pilot's head in order to force the pilot to have them leave Mother Base.
Some time afterward, the helicopter was forced to make an emergency landing 50 miles into the African mainland due to running out of fuel. On Eli's orders, the children then proceeded to tie him up with vines and duct tape as a message to Diamond Dogs, having anticipated that they are hunting them down and wanting to challenge them. He was ultimately rescued by Diamond Dogs, although he had suffered extreme dehydration due to his situation by the time he was rescued, requiring that he be hospitalized by the time they found him.
Behind the scenes
The chopper pilot is a minor character in Metal Gear Solid V: The Phantom Pain. He was originally supposed to have a slightly more major role, being rescued around the time of the Kingdom of the Flies mission, although because the mission itself was cut, he was only seen in the final version being forced to fly the child soldiers away from Mother Base.