In early 2015, Hideo Kojima was forced to leave Konami behind, with his latest Metal Gear game, “Metal Gear Solid V: The Phantom Pain” nearing completion-but reportedly Konami wasn’t happy with the money going into the project, and the possibility that it might have needed more development time. So several features were cut short to meet the September 2015 deadline-including a third ending to the game, “Kingdom of the Flies”.
Technically, the game, like it’s predecessor Peace Walker, has two endings, or endings to two “acts”. The first one is where Venom Snake-having gotten his revenge against Skull Face-and Diamond Dogs watch as the dormant Metal Gear sehalanthropous is loaded unto the R & D platform at Mother Base. This ending has the scene where my header image comes from…
Act II deals with an outbreak of the human vocal cord parasite on Mother Base, as well as Eli-the future Liquid Snake and clone of the real Big Boss-escaping along with Sehelanthropus and the child soldiers (including Psycho Mantis, who uses Eli’s anger toward his “father” as a sort of conduit), setting up a possible future confrontation (and not the one in MGS btw).
However, this isn’t followed up on, and after Quiet leaving and a replay of the first mission from a slightly different perspective, we’re given an ending which reveals that Venom is not, in fact, the “real” Big Boss but a decoy-a helicopter medic who has been brainwashed and altered while the real one goes into hiding and builds up FOXHOUND and Outer Heaven-although he’s still got a role to play, helping to build the legend of Big Boss-and eventually confront Solid Snake at Outer Heaven.
However, there was in fact a third ending planned. This would answer the question of what exactly happened with Eli and Sehelanthropus, and provide more of a link of sorts with the original Metal Gear Solid.
In this ending/mission, Diamond dogs track Eli and the MG to an island in Africa. However, Eli-reaching puberty-is infected with the vocal cord parasite and will die and infect others if he gets out. Plus, XOF (Now working with CIPHER again with Skull Face gone) wants their Metal Gear back, and are also on the site.
The stage is set for a massive final battle, which would’ve incorporated more of Diamond Dogs (Presumably in addition to your regular backup buddies or Peqoud) taking on the Metal Gear.
Ultimately the MG is destroyed for good-Eli is nearly killed by XOF soldiers-and a accidentally colorblinded Venom Snake….
But unfortunately, Eli is showing symptoms of the virus, and Venom and Diamond Dogs are forced to leave the infected Eli behind on the island as they sterilize it with napalm-but then Eli’s buddy Psycho Mantis shows up, curing Eli and lifting him off the island just in time.
While Venom Snake and his crew watch from above (with Snake’s bloody reflection and shrapnel horn showing that he’s fully become a “Demon”-a common theme in the game) Eli states that “Not yet-it’s not over yet” as an image of New York appears. The two of course would go on-along with former Diamond Dogs member Revolver Ocelot -to be members of Liquid’s incarnation of FOXHOUND, and challenge Solid Snake at Shadow Moses.
The ending echoes not only the New York setting of Metal Gear Solid II (although it’s a bit unclear why) but also Liquid’s later line in the first Metal Gear Solid. The line is also said by Olga, Volgin, Solid Snake, Liquid Ocelot, Paz, the Peace Walker weapons etc. as is a sort of trope of the series, along with “You’re pretty good” “Metal gear?” and “Kept you waiting, huh?”)
However, it was over, and apart from concepts and some cutscene work-with voice-acting as well recorded-the mission was not included in the final release, nor in the definitive edition re-release. There are still fans who hold out hope that someday, somehow it will be finished; but there seems to be no indication of that happening.