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After escaping Mother Base with Tretij Rebenok and the Mbele Squad, and possessing the English strain of vocal cord parasites and Metal Gear Sahelanthropus, Eli took over the island. XOF scouts sent to retrieve Sahelanthropus were infected by Eli, spreading the parasites across the island and driving the adults away.
Eli goaded Venom Snake into coming for him by leaving a cassette tape. Eli presented that they had one demand in exchange for Sahelanthropus and its nuke: the body of "Big Boss." However, Eli's voice had begun to mature. By the time Snake arrived on the island, XOF troops had already begun a strike to kill Eli and take Sahelanthropus back. Many of them had been killed by booby traps set by Eli's boys, but a number of them had survived.
Snake made his way to the center of the island, where he found Eli resting in Sahelanthropus' cockpit among the child soldiers. However, a squad of XOF soldiers had beaten him there, opening fire on Eli. Their weapons were rendered useless by Tretij Rebenok's psychokinesis. Eli activated Sahelanthropus and began killing the soldiers. He eventually discovered that Snake was hiding from the attack. He stopped his onslaught momentarily to speak with Snake and declared that he was going to get his revenge, and the two then began their battle.
The ensuing conflict between Diamond Dogs, XOF, and Sahelanthropus was catastrophic, nearly destroying the whole island. Their battle came to a close when Sahleanthropus' was rendered inoperable, and Eli and Tretij Rebenok defeated. As Eli emerged from the cockpit, he was approached by another squad of XOF soldiers who were ready to kill him. Snake sprung a surprise attack on the would-be assassins. However, during the attack, he accidentally shot Eli after a close-proximity explosion confused his senses.
Upon Ocelot and the rest of Diamond Dogs' arrival to clean up the island, it was discovered Eli hadn't died, as he had donned a bulletproof vest. Snake ordered that he be returned to Mother Base in order to be patched up. However, Eli suddenly began showing symptoms of the English vocal cord parasite's effects. Eli expressed his hatred for Snake and Cipher, claiming that someday he would destroy Big Boss, believing Venom Snake to be his father. With the island completely contaminated by the parasites, Ocelot ordered the entire island to be hit with a napalm strike to burn every last thing on it. As Diamond Dogs began to retreat with the salvaged remains of Sahelanthropus, Snake gave Eli a pistol with one bullet in it. Watching his "father" depart, Eli turned the pistol on himself, but was stopped by Tretij Rebenok. Tretij Rebenok used his psychokinesis to remove the English strain from Eli's vocal cords. He then levitated Eli and himself away from the island to escape the napalm strike.
The island was destroyed in the napalm strike, killing all life on it.
Behind the scenes
Kingdom of the Flies was originally going to be the setting for the mission of the same name in Metal Gear Solid V: The Phantom Pain. However, the location and the mission itself was removed from the final version due to time constraints. The location is mentioned in the game's ending timeline and appears in the "Phantom Episode" on the Metal Gear Solid V: The Phantom Pain - Collector's Disc.
- Metal Gear Solid V: The Phantom Pain (mentioned)