Players play as Solid Snake using the keypad on the phone. Gameplay is a combination of Metal Gear Solid 2 and Metal Gear Solid 3. 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. The camera also controls the in-game camera, and will also be able to aim Nikita missiles. Hanging off ledges and hiding in lockers will also be possible. VR missions are also included.
The story takes place between Metal Gear Solid and Metal Gear Solid 2, and follows the early days of Philanthropy. Ocelot has leaked all the technical information for Metal Gear REX onto the black market. As a counter-measure, Solid Snake and Otacon form Philanthropy. It isn't long until Otacon receives his first lead on development of a new Metal Gear. Victoria Reed, an AI (artificial intelligence) programmer, learns that the technology she has been developing will be used in a fearsome weapon of destruction. She becomes a whistle-blower and attempts to escape from the facility. She places her trust in Otacon, and now Snake has been dispatched on a solo mission to infiltrate the facility and rescue the scientist.
Upon reaching the facility it becomes evident that the military holding the plans for the new Metal Gear REX is non-aggressive. Despite this, Snake infiltrates the facility and eventually reaches the basement, where he is captured in a cell. Snake is contacted via codec frequency 116.66 by the terrorist leader, named simply Commander, and it is revealed to the player that Victoria Reed was an AI program herself (Victoria Reed's initials are VR), created by the terrorists to lure Snake into the facility and deactivate their security system, allowing the terrorists to essentially walk right in and commandeer the REX stored in the basement. Snake escapes his cell and makes his way to the REX, avoiding the Semtex charges now lining most of the base and machine-gun mounted sentries along the way.
En route to the basement, Snake uses C4 to open a cracked wall and when he walks through the newly formed hole, the room flashes green and blue and becomes blurry and artificial. Strange codec calls come in from not only Otacon, but also Commander, breaking the fourth wall and urging the player to turn off their cell phone. The real Otacon then contacts Snake, alarming him that he has been drugged and kidnapped and placed into a virtual reality simulation, and he is in the process of hacking the simulation to save Snake. He says that he's been trying to reveal the identity of the group that kidnapped him, but has been unable to do so, however, due to the technology used in the VR simulation. He comments that judging by the complexity of the program, the programmers must have near-unlimited resources, hinting at the group being The Patriots. He then remarks that since Snake is so far into the simulation, it may be easier to just complete the objective and destroy the fictional Metal Gear than to even bother hacking him out. Snake agrees, encounters Commander on top of a VR Metal Gear REX, and easily dispatches him using a combination of the FAMAS and Nikita rocket launcher.
Snake then wakes up to unnamed voices speaking. They say that while Snake did prove useful, he failed to provide them with the battle data they needed for the Project, and they instruct someone to erase all memories of the simulation and dump him back where they kidnapped him. One unnamed voice then says that they already have the second test subject lined up. One of the voices then says, "...Let's see if Jack can do better."