Lobito Island Incident

In 2016, a jumbo jet carrying Senator 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.

"Briefing"
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.

"Undercover Action"
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.

"Egersis"
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 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 assisstance 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.

"Dream Land"
Snake later found the real Teliko at Ebro Tower, and was also confronted by a mysterious doppelganger, who soon disappered. 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.