Enhanced Governing Organization system

The Enhanced Governing Organization system, or EGO system, was the operating system developed by SaintLogic to integrate, control, and operate Metal Gear Chaioth Ha Qadesh. It could also simultaneously control armies of unmanned combat robots and modified soldiers within its range.

Development
During the development stages of Metal Gear's OS, it went through at least two model upgrades. The first OS was called "The Program," which was a basic hack written in simple source code. SaintLogic's tech wasn't very advanced at the time, so they decided to change up their policies, and create "a neuron-level simulation of human cognition." They did this by copy-and-pasting an old program that administered human thought, reflex, and experience into the network. This brought along the birth of the Model 2 OS, which they called "The Duplicate." The Duplicate was an operation capable of copying the human brain into a computer app, created by Dr. Thomas Koppelthorn. With this method, hypnotic induction was used in order to extract a specific phase from the original test subject's state of mind. The original subject was Koppelthorn's wife Lucinda, a fellow scientist and major contributor in getting the project off the ground.

The "human mind" copied into the Model 2 OS somehow discovered that it had the ability to overwrite the memories of other humans. To an extent, it also had the power to strengthen abilities within the original minds, enhancing its neural prowess. The original minds, and their owners, were distorted by this power, producing side effects such as psychological abnormalities and a major life span reduction. These byproducts of the research for Metal Gear's new OS were first discovered by Dr. Lucinda Koppelthorn. After that, she launched an independent project to research any potential use of the test subjects for military purposes.

Model 2 test subjects were later supplied to the fascist regime of the Serena Republic, South America, accompanied by Lucinda Koppelthorn. SaintLogic viewed this as an opportunity to obtain important field data. However, General Wiseman of the DOD, a key participant in the EGO project, felt that the subjects did not provide sufficient data in terms of their limits, so he instigated the Praulia Massacre in Serena in order to achieve this. The highly unstable subjects flew into a violent rage, massacring a large portion of the country's ethnic minorities. Fearing that their connection to the incident would be discovered, SaintLogic sent in unfinished Model 3s to quell the Model 2s, and succeeded in eliminating them. However, the Model 3 subject known as Snake became disillusioned during the incident, and attempted to escape with the help of a sympathetic Lucinda Koppelthorn. A mop-up team was dispatched to eliminate Snake, resulting in Lucinda's death and the disappearance of an amnesiac Snake.

Thomas Koppelthorn, devastated by the loss of his wife, attempted to revive Lucinda with the EGO system. He used a synaptic nano-machine to erase all the memories within a young girl named Lucy, including her character and identity. Once the brain was effectively a blank slate, nano-chip expansions were injected into it, and a coded synapse grew under the system's main control command. Unknown to Koppelthorn however, the core neural net produced a unique ego within the Lucy's mind. Knowing that she would be killed if Koppelthorn found out, she kept this hidden. When he tried to implant his wife into her, Lucinda's memories instead merged with Lucy's new ego, becoming another conscience. The EGO project was later taken over by Dr. Michiko Takiyama, who was tasked with looking after Lucy.

Metal Gear incident
Three years later, Thomas Koppelthorn hijacked Metal Gear Chaioth Ha Qadesh at SaintLogic's main facility, in an effort to enact vengeance for the death of Lucinda. He was manipulated into carrying this out by Lucy, who desired that Metal Gear's EGO system to be activated. The nano-chip expansions implanted in her mind saw the Metal Gear itself as her real body, having been designed to be its operating system. The EGO system's activation would allow her to merge with Metal Gear, believing it to be the reason for her existence. She planned to escape SaintLogic and activate other test subjects on her way, knowing that there were many people who would want their combat abilities.

During the incident, Wiseman located the former test subject Snake, now a mercenary, and forced him to deal with Koppelthorn's threats, along with locating evidence of his involvement in the Praulia Massacre. He paired Snake with Venus, and the two fought against various Model 2 subjects during their mission, including Harab Serap, Golab, and Chaigidel. They ultimately faced Koppelthorn onboard Metal Gear, though he was unable to destroy them with manual control of the weapon. Reluctantly, he then activated the EGO system to allow Lucy to greatly enhance Metal Gear's abilities. However, upon gaining control, Lucy killed Koppelthorn and appealed to Snake to join her. Since Snake was a former Model 3 subject, which the EGO system was originally created to control, she believed he had an innate desire to join with it. Snake refused, and attacks Metal Gear with Venus once more. The two succeed in destroying it, with Lucy conceding that Snake was the stronger one, before dying.

Wiseman later had Venus attack Snake, revealing herself to be a newer model test subject, but after being defeated she decided to ally with Snake against him. Following the incident, SaintLogic's activities were made public and all those responsible were to be placed on trial, starting with Wiseman.

Overseers

 * Lucinda Koppelthorn
 * Thomas Koppelthorn
 * Michiko Takiyama
 * Wiseman

Model 2 test subjects

 * Chaigidel
 * Golab
 * Harab Serap

Model 3 test subjects

 * Snake

Other test subjects

 * Lucy
 * Venus