|This article is about a non-canonical topic in the Metal Gear series.|
In 2016, a jumbo jet carrying Senator Viggo Hach, an important politician and likely future presidential candidate, was hijacked by terrorists. In exchange for the senator, the terrorists demanded "Pythagoras" from the United States government; a research project that was being conducted on Lobito Island in the Moloni Republic, southern Africa. In efforts to identify these terrorists, the government began an investigation of Pythagoras.
The Moloni government refused to cooperate and work with the United States, saying that it didn't want interference in its current affairs. In response, the U.S. sent in an HRT special forces unit to investigate, but the team was obliterated by armed resistance, with the sole surviving operative, Teliko Friedman, taken captive. With no other options and time running out, the U.S. government called Solid Snake to infiltrate the island's laboratory, discover the nature of Pythagoras and to rescue Senator Hach.
Commanded by former CIA agent Roger McCoy, Solid Snake successfully infiltrated the Lobito Physics and Chemistry Lab. An FBI-recommended psychic, Alice Hazel, was also assigned to help in the mission, though Snake was initially skeptical of her abilities. Snake eventually met a lone man in a control office called Gary Murray. Gary helped Snake to find Dr. Flemming by telling him of his last known location. Snake then headed to the residential block to find Flemming.
Meanwhile, two talking dolls, named Elsie and Frances, terrorized the hostages on board the captive passenger jet, Flight 326. Frances proceeded to kill the pilot and co-pilot, carving the numbers "1" and "14" on their chests, and transmitted photographs of them to the U.S. government.
Reaching the eastern building of the residential block, Snake intended to create a false identity on a nearby security computer, in order to access the building's rooms. To Snake's surprise, his profile was already registered under the name "Hans Davis." After finding a decoy Flemming, Snake was ambushed by Lieutenant Leone, the leader of the mercenaries occupying the facility. Murray had apparently led him into a trap. Teliko then rescued him using a stun grenade as a diversion, and helped him to escape. After a brief exchange Snake and Teliko joined forces, though Snake soon began to suffer severe headaches.
Roger informed the two that Hans Davis had been Flemming's supervisor several years ago, and had presided over various research projects. He had been on loan from BEAGLE as a lab chief, but had no records on file before that. When Hans had first arrived, witnesses attested that dozens of children had been taken from the mainland to Lobito Island by boat, an image eerily reminiscent of "The Pied Piper of Hamelin," having been used to test a new form of drug. Gary contacted the group by Codec and informed them that the drug was called ACUA and that Pythagoras was a Metal Gear. Gary had apparently wanted to gain the ACUA research data from Flemming and was willing to kill him after he was finished.
Splitting up from Teliko temporarily, Snake found the real Flemming and discovered that he had been "Gary" all along. Flemming then claimed that Snake was Hans Davis, with Snake beginning to struggle against Hans' memories and personality. Flemming informed Snake that BEAGLE had needed a role model for the test subject children, and that Snake had agreed to fill the role, having been eager for someone to follow in his footsteps. Snake had become Hans, who after a while, had decided to create false memories to forget he was ever Hans in the first place. Flemming then revealed that his daughter was on Flight 326, which had been hijacked by No. 16, one of the former test subjects on Lobito, and that the numbers being carved onto the hostages were a coded message to Snake out of spite.
Teliko eventually found Snake and shot at Flemming, causing him to flee and leave behind the heavily encoded Pythagaros data. Teliko persuaded Snake that since he cannot be trusted she should hold onto the disc and he reluctantly accepted. It was around this time that Roger received a call from his superior Charles Schmeiser who was suspicious of why Roger had been so eager to participate in the mission, and why he had requested Snake to join them. Schmeiser was also suspicious of Snake's link with BEAGLE and informed Roger and Alice that they must prepare for the possibility that Snake was losing his mind.
As Snake and Teliko headed back to the storehouse they were ambushed by Leone who claimed to have a grudge with BEAGLE, and that he had received an anonymous tip that stealing the Pythagoras data would enable him to exact revenge. Since Snake and Teliko had made things difficult for him, he decided to attack them both. Snake and Teliko eventually outran Leone with assistance from Alice, and attempted to chase Flemming to "Flemming's Assembly Room," the main lab complex on Lobito Island. As they crossed the bridge to FAR, Teliko shot at Snake, revealing that she was really a BEAGLE-hired assassin named La Clown, and escaped with the Pythagoras data.
Snake later found the real Teliko at Ebro Tower, and was also confronted by a mysterious doppelganger, who soon disappeared. Snake and Teliko then battled, each convinced that the other was an enemy, in an enclosed board game-style room created by La Clown. Snake won the fight, and after convincing Teliko of his affiliations, they teamed up. The two escaped just as La Clown blew up the room.
Afterwards, Snake and Teliko decided to ally themselves with Leone in order to stop Flemming. Leone and his troops prepared to enter FAR, while Snake and Teliko shut down the powerhouse in order to allow them access. However, Flemming and his ACUA soldiers ambushed the group and captured Leone. Snake and Teliko were later forced to kill Leone after he became subjected to the drug ACUA.
Entering FAR via an alternative route, Snake and Teliko are again attacked by La Clown. Maintaining Teliko's appearance, so that Snake had trouble telling the two apart, she also used her hypnotism to "create" more copies of herself in an attempt to turn the battle in her favor. However, Snake and Teliko eventually managed to defeat Clown. Teliko recognized Clown's perfume and realized that she had been the killer of her father, Collin Friedman. Snake and Teliko then took the Pythagoras data from her corpse and left her where she died.
"Vs Metal Gear"
Snake and Teliko eventually encounter Metal Gear KODOQUE, piloted by Flemming. Flemming had been blackmailed into following No. 16's order, due to his daughter Constance being on board Flight 326. However, he felt that No. 16 had no intention of honoring her word, and threatened to nuke a pristine island in the South Pacific that she had dreamed of, after killing Snake. As Flemming activated Metal Gear, Teliko gained access to the machine's interior. While Teliko disrupted its weapons fire and warded off Patrol Bots, Snake used heavy weapons to disable the towering mech. When Flemming exposed himself, Teliko managed to shoot and kill him, thwarting his plans.
Towards the conclusion of the incident, Alice was revealed to be No. 16, who was capable of using ACUA to control people's thoughts. It was she who caused Snake to come under suspicion, by implanting the memories of Hans Davis into his mind. After Snake and Teliko successfully destroyed Metal Gear, the memories of all the people Alice had controlled came back to her simultaneously, causing a shock which led to her death.
Meanwhile, Constance Flemming turned the tables on terrorist collaborator Lena Arrow, the murderous puppeteer behind Elsie and Frances, on board Flight 326. The unassuming girl attacked a surprised Lena with a knife, revealing herself as No. 104, another Lobito test subject whose mind now inhabited Constance's body. She then considered carving the number "104" onto Lena's bones, as the latter had done to the other murdered passengers on board
With the terrorist threat foiled, Teliko and Snake successfully escaped the complex on Lobito Island.
At some point afterwards, the Secretary, Chairman, Secretary General, Prime Minister, and the President of the United States held talks to discuss the events of the incident, due to the serious nature of the incident. The president arrived at the meeting late due to the United States Coast Guard being too enthusiastic. The unexpected events of the mission also resulted in the meeting being held on short notice. After some deliberation, the five decided to do something drastic enough that the Secretary General mentioned they'd have to be the "bad guys," before discussing other matters and then being dismissed until the next meeting within six months.