Kojima hasn’t lied to you; Metal Gear Solid 5: The Phantom Pain is not the complete project he planned it to be. Kojima isn’t keeping any secrets about The Phantom Pain either.
The PlayStation 4 Collector’s Edition has a bonus disc, which actually contains an alternate ending. When you see what’s in the ending, we think you will agree that it provides better closure to the Metal Gear saga, or at least it would if this made it to the final game.
Spoilers abound below so read at your discretion. For the purposes of simplicity, we’ll also make it brief and to the point.
This section of the game, episode 51, is called Kingdom of the Flies. Eli, the child soldier destined to become Liquid Snake, has taken Sahelanthropus, Psycho Mantis, the vocal cord parasite, and his child army, to a deserted island, where he has established himself Lord of the Flies style, a small kingdom.
Eli is himself infected with the dreaded virus, and Cipher is close to their tail. Big Boss, mixed feelings and all, chases after him to the island with XOF in tow. After taking out a lot of XOF soldiers, Eli is reunited with Big Boss, with Eli expressing his intent to kill Cipher, and of course, the Boss.
After a large battle, the Boss faces a moment of regret. Changing his mind at the last minute, he shoots at the XOF soldiers to save Eli. In the heat of a conflagration, he mistakenly shoots Eli and thinks he kills him.
This all means nothing in the end. When Kaz arrives, he points out Eli was saved by a bullet vest, but is hit by the parasite anyway. XOF leaves Eli to die, with some last choice words between pseudo-father and son.
As a final twist, Psycho Mantis reappears, psychically removing the parasite from Eli’s body and rescuing him. Mantis and Eli survive to appear in the other Metal Gear Solid games.
You can watch the fully planned sequence above.