The game and manual warn that using this device for extended periods of time may lead to eyestrain, and prolonged use is not recommended.

The manual that is included with the American version of the game is significantly thinned down, and as such, does not contain a specific guide on how to utilize this feature.

Snake's initial objective is to infiltrate a research facility operated by SaintLogic (called "StrateLogic" in the Japanese version), a military arms manufacturer, located on an isolated North American island.

Shortly into Snake's mission, Dalton's authority is exceeded by General Wiseman, an official with the United States Department of Defense.

Snake slowly learns that Wiseman's involvement is in response to a SaintLogic executive Thomas Koppelthorn, who has made demands that the United States release several prisoners and has threatened to use nuclear weapons.

It later becomes evident that Koppelthorn is seeking revenge for an incident that occurred three years before, and among his demands are that the United States release Snake to him.

Before crossing to the building where Koppelthorn is located, Snake and Venus are met by Metal Gear Kodoque from the first Acid which was rescued before being destroyed during the events of the last game.

Lucy then declares the truth about Lucinda, who had helped Snake to escape SaintLogic and wanted to die because of her inhumane actions.

At this time Wiseman was to have Venus work her way through SaintLogic and recover the Lucinda File, and place any blame on Dalton and Snake.

Venus and Takiyama escape the building safely, and outside SaintLogic witness Metal Gear Chaioth Ha Qadesh return to life.

The U.S. military, which has been called in to secure SaintLogic, fires upon Metal Gear and a missile from its rear launches, and lands in the ocean a short distance away.

The game ends with Dr. Takiyama and Venus safely recovering from the SaintLogic incident, with General Wiseman arrested and facing charges of war crimes.

Snake, who has recovered extremely quickly, is confronted by Dalton, who provides him with a United States identity, his friends, and $15 million.

In the North American and European versions, several illustrations that accompany the end credits show what happens to the game's main characters after the incident.

Wiseman is shown being led away by law enforcement personnel, but his manner remains undaunted, implying perhaps that there is yet a way for him out of his predicament.

And in a vignette that could have been taken much later after the events of the SaintLogic incident, Venus is seen manning the checkout counter at a supermarket, hinting at her quiet assimilation into everyday life.

The remaining four were fan made submissions selected in a Konami sponsored contest by four online publications (Game Informer, IGN, GameSpy, and 1UP.com), which were an alternate Naked Snake card from MGS3, a Banana Skin, Possessed Arm, and Emma's Parrot.

The game's soundtrack was composed by Akihiro Honda, Hiroshi Tanabe, Nobuko Toda and Shuichi Kobori.