After the events of MGS3: Snake Eater, Snake has distanced himself from the USA and, together with Kazuhira Miller, founds the Militaires Sans Frontières (MSF). When a mysterious professor and his student Paz request help to confront a secret military force established in Costa Rica, Snake accepts the mission after hearing a recording of the voice of The Boss, his mentor, who is believed to be dead.

As the story unfolds, Snake discovers the Peace Walker project, an autonomous nuclear weapon with artificial intelligence, designed to function as the ultimate deterrent. The plot delves into philosophical questions about peace, freedom, and the concept of deterrence, while Snake faces the shadows of his past and the legacy of The Boss.

The gameplay combines stealth action with base management, soldier recruitment, and weapon development, while also supporting co-op missions. Peace Walker is a crucial link in the Metal Gear mythology, bridging the story between MGS3 and The Phantom Pain, and marks Snake's transition into the legendary role of Big Boss.