Metal Gear Solid V: Ground Zeroes takes place in 1975, several months after Metal Gear Solid: Peace Walker and nine years before Metal Gear Solid V: The Phantom Pain. After Paz's disappearance, intel finally reports that she is alive and detained at Camp Omega in Cuba. Chico attempts to rescue her and gets captured too, forcing Big Boss to infiltrate Camp Omega to save both Paz and Chico.
The game is essentially a prologue to The Phantom Pain.
In the aftermath of the Peace Walker incident, Paz Ortega Andrade is missing and presumed to be dead. Under the direction of Kazuhira Miller and Huey, Militaires Sans Frontières turn their attention to an upcoming inspection by the UN amid suspicions that they possess a nuclear weapon, which MSF believes to be an attempt by the Cipher organization to stifle and retaliate them. Their preparations are interrupted when MSF agents in Cuba investigate reports that Paz survived and has been detained at Camp Omega. Futhermore, Ricardo "Chico" Valenciano Libre attempts to rescue her and is similarly captured. Believing that both of them could compromise MSF, Snake is sent to infiltrate Camp Omega and extract them if they are alive, or confirm that they are dead and if so, determine what they revealed to their captors. Snake also recognizes the value in rescuing Paz, as he believes doing so will convince Cipher to stand down while Paz will be more willing to discuss Cipher's activities with MSF.
Snake infiltrates Camp Omega as a mysterious Special Forces unit known as XOF simultaneously departs via helicopters. He locates and extracts Chico, who claims Paz is dead. Using a recording that Chico gives him, Snake and Miller deduce that Paz is alive, and was moved deeper into the camp. By collecting audio cassette tapes around the base, Snake learns that Paz and Chico were tortured, physically and psychologically, for information about the MSF base. Chico, after being tortured and forced to sexually assault Paz, tells Skull Face the location of the base and what defenses there are. In a later recording, Paz is heard calling Chico a "coward" and "traitor" for giving up the information; however in the final tape she records herself saying she forgives Chico and would not have made it through the torturous interrogations without him.
Snake ultimately manages to rescue Paz as well, with the group escaping via an MSF helicopter designated Morpho One. However, on the way back to Mother Base, Chico discovers that Paz was surgically implanted with a bomb, prompting Snake and an MSF medic to remove it by hand. They then arrive to Mother Base to see it in flames as XOF forces attack. Morpho One lands long enough for Snake to rescue Miller, who claims that the UN inspection was nothing but a ruse for the XOF ambush, which razes Mother Base. As they attempt to escape XOF, Paz regains consciousness and warns everybody that there is a second bomb inside her body. Knowing that she is about to die, she jumps out, trying to throw herself clear of the helicopter. She succeeds, but the explosion causes Morpho to spiral out of control and collide with a pursuing XOF helicopter. Snake is knocked unconscious.
The epilogue reveals that the United States government downplayed MSF's destruction and attempted to cover up their dealings with the organization, as do many of MSF's clients. There are no known survivors of the assault, apart from Snake, Miller, and Huey.
In a post-credits scene, set prior to Snake's arrival at Camp Omega, Paz is being interrogated by Skull Face, who demands the whereabouts of Cipher / Zero, as Paz had met Zero in person. Paz eventually gives in and agrees to tell him Zero's location before the scene ends.
