Snake is contacted via Codec frequency 116.66 by the terrorist leader, named simply the Commander. Despite this, Snake infiltrates the facility and eventually reaches the basement, where he is captured in a cell. Upon reaching the facility, it becomes evident that the military holding the plans for the new Metal Gear REX is non-aggressive. She places her trust in Otacon, and now Snake has been dispatched on a solo mission to infiltrate the facility and rescue the scientist.

She becomes a whistle-blower and attempts to escape from a black ops military research facility. Victoria Reed, an AI (artificial intelligence) programmer, learns that the technology she has been developing will be used in a fearsome weapon of destruction. It isn't long until Otacon receives his first lead on development of a new Metal Gear. As a counter-measure, Solid Snake and Otacon form Philanthropy. Ocelot has leaked all the technical information for Metal Gear REX onto the black market. The story takes place between Metal Gear Solid and Metal Gear Solid 2, and follows the early days of Philanthropy. The game has the fewest boss characters in the overall series, only having one. Hanging off ledges and hiding in lockers will also be possible. The camera also controls the in-game camera, and will also be able to aim Nikita missiles.

For example, the player can take pictures using the phone's digital camera and transfer them onto Snake's sneaking suit, creating an all new camouflage to wear. Gameplay is a combination of Metal Gear Solid 2 and Metal Gear Solid 3. The player controls Solid Snake using the keypad on the phone. Screenshots from the Japanese version of the game.

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