Ground Zeroes Incident

A Trojan Horse operation was carried out by the paramilitary force XOF to destroy Militaires Sans Frontières and its leader Big Boss, due to the mercenary group's growing strength.

Inspection preparations
Around late February 1975, MSF received a letter from the IAEA requesting that they inspect Mother Base, allegedly due to their ordering nuclear fuel from Uzbekistan officials. Big Boss and Kazuhira Miller both realized that the IAEA had been manipulated by Cipher and the real reason was to locate Metal Gear ZEKE's nuclear warhead as revenge for foiling their plan via Paz Ortega Andrade earlier. Although they attempted to refuse the inspection, Dr. Huey Emmerich had secretly sent a letter indicating that they changed their minds.

Forced into a situation where they either allow the inspection to occur or draw unwanted suspicion if they had a third "change of heart," Big Boss and Miller rushed to prepare for the inspections. This included sending all civilians save for Huey (which included the French ornithologist Cécile Cosima Caminades) back to their home countries, as well as sending all their amored vehicles except for ZEKE to the shore alongside any rebellious personnel for mandatory R&R. Any remaining Sandinista soldiers at Mother Base were sent to regroup with Amanda Valenciano Libre at Cuba (also extending her assignment thanks to the upcoming inspection), and the remaining personnel were told the truth to ensure no one accidentally exposed the existence of either ZEKE or its nuke. The one silver lining in all of this was they didn't need to worry about Dr. Strangelove divulging the existence of ZEKE or the nuke, as she had already resigned from MSF and left Mother Base the week before.

Word of Paz's survival
On March 6, 1975, Miller revealed that, thanks to both intercepted reports from Cipher as well as Amanda, they discovered that Paz was still alive. Miller suggested that they retrieve her, in order to get information on Cipher's true nature, as she was their sole viable link. However, because of the inspection, MSF was forced to put it off until afterwards, and hoped to send Chico to meet with his sister to distract him, as word was already spreading about her survival. Unfortunately, Chico never made it to Havana; he had snuck off the ship he was to be delivered on while it was refueling at Santiago de Cuba and travelled via a three-day hike on the 60 mile mountainous expanse between Santiago and the prison facility Paz was held at. He then attempted a rescue of Paz, narrowly evading several choppers, but ended up caught when he found a prisoner who resembled Paz, resulting in his capture. Miller later discovered this from both Amanda and Big Boss, and ordered for the Intel Team stationed at Cuba to find Chico.

Chico's imprisonment


Chico was imprisoned at Camp Omega, which contained animal cages, and also had bolts installed into his achilles tendon. A few days later, during a routine torture session of Paz, Chico was taken with the group, XOF, to the Admin building, where he met the group's leader, Skull Face. Skull Face informed Chico that there was no hope for escape, unless he was to submit to interrogation regarding Mother Base's defenses. After several interrogations, including beatings, watching Paz get stripped, raped, and beaten, and then forcing Chico to have sex with Paz while Skull Face watched, Chico, broken from the torture, relayed everything he knew about Mother Base, including confirmation about ZEKE's existence. He then was locked back up, and then forced to torture Paz. Skull Face, knowing Big Boss and MSF are most likely going to try to find Chico and possibly Paz, then had Chico send a SOS signal explaining where he and Paz were. True to Skull Face's predictions, Big Boss and Miller realized it was most likely a trap, but were left with no other options but to rescue Chico and Paz.

After preparations, including doing a flight path and prepping a bird as well as final briefings on the location site, Big Boss then departed for the coastline of Cuba, with the only backup being a sole extraction chopper to arrived once he rescued Chico and Paz, alongside presumably any other prisoners he managed to find. Skull Face, however, still had unfinished business with Paz. He revealed that Paz was the only Cipher agent who actually met Zero face-to-face, and as such she knew his location, and he wanted her to divulge his location to him, as he intended to liberate himself from Cipher. After getting his location after implying that this might help Big Boss, Skull Face also put a bomb in Paz's stomach and another bomb inside an undisclosed part of her body, anticipating the likelihood that Big Boss would attempt to rescue her.

Rescuing Chico


Two days later, on March 16 at 00:00, Skull Face paid a final visit to Chico's cell, and gave him back his Walkman. After telling Chico that "[Paz] didn't suffer long," he told Chico to give his regards to Big Boss when he arrives. Skull Face then departed for the heliport alongside XOF. After masking the chopper's XOF logo with a strange light, he then commented that the "trojan horse" was a go and had the group depart. He then ordered for all of the XOF personnel to dispose of all their XOF patches. However, nine of those patches survived, one of which landed on Big Boss's posterior while he was scaling the cliff. Big Boss then travelled to Camp Omega after noticing its location on the iDroid, evading patrols and watchmen. After knocking out the guards near the area, he then found Chico in his cage, although Chico ended up panicking at the sight of him, forcing Big Boss to put him in a sleeper hold due to it otherwise drawing the guards to him. He then took him to the extraction site.

Retrieving Paz
After setting him down at the extraction site, Chico informed Big Boss that Paz was dead after showing him his walkman tape of her interrogation, reaffirming it when he was asked for her location. Undeterred, Big Boss managed to deduce Paz's location from the tape sounds, tracing her to the basement of the Admin building of the base. He then found her strung up to the boiler room. After making sure she was alive, he then cut her loose and took her with him. All the while, she was talking in her sleep about disturbing events. He then returned to the extraction site with the base now searching for the missing Paz, and managed to load Chico and Paz onto the chopper and left.

Attack on Mother Base
On their way back to the base, Chico discovered Paz had a scar on her gut and warned Big Boss. Upon seeing the scar, Big Boss ordered for a medic to come to her. Realizing from the scar that she was most likely rigged with a bomb by her captors, they were forced to operate on Paz immediately, not having any time for anesthetics due to the unexpected discovery. During the surgery, Huey informed Big Boss that the inspection was a success and that they have not found ZEKE. Eventually, they found the bomb which allowed them to remove and dispose of it.

However, the chopper lost contact with Mother Base, with Big Boss soon discovering why: it was under attack by the XOF forces. He then returned to one of the struts and aided Miller and the others in escaping, also shooting down an XOF chopper. However, the strut was about to collapse due to C4 being placed on the struts. They then rushed to evacuate with only Big Boss, Miller and a single MSF soldier able to escape, the rest having been gunned down by the surviving XOF soldiers. Retreating from the crumbling Mother Base, Miller interrogated Paz out of anger at the losses MSF had suffered when Paz revealed that she had been implanted with a second bomb, and jumped out of the chopper to save them. Unfortunately, she jumped out too late as the explosion caused it to careen into a pursuing XOF chopper.

Aftermath
The attack on Mother Base was so damaging that smoke could be seen from far away. The media reported them as being "money-hungry private militias" and a scandal ensued when the United States and its allies were discovered to have been clients of MSF, although the Secretary of Defense denied their involvement in the incident, and the other nations among the client's list refused to comment either way. Similarly, the UN and the IAEA were mentioned to have done an inspection on that day, yet they too denied any involvement. There were no reported survivors, although choppers were seen in the area both prior to and after the incident.

Big Boss, Miller and the MSF medic were evacuated to Hospital Mena de Barranquilla in Barranquilla, Colombia to have their injuries treated, where Big Boss and the medic fell into a nine year coma on 13:31. When Miller inquired about the latter's status, the hospital staff hesitantly informed them that the medic suffered shrapnel to his head. Huey also survived the events of the operation. Chico, the unidentified MSF Soldier, Morpho, and his co-pilot were killed in the helicopter crash.

Members who weren't at Mother Base at the time of the attack had been cut off and decided to branch out and form their own Private Forces or joined Miller in reforming MSF into Diamond Dogs who then relocated to their new Mother Base located in the Seychelles. One in particular, Mosquito, was forced to go into hiding in total isolation out of paranoia that XOF would send a clean-up crew after him when he survived Mother Base. In addition, he would later believe thanks to disinformation that Big Boss sold out the MSF due to his commander being absent at the time of the attack. At least ten others would also scatter, although they grew to become even more unhinged, behaving erratically until Venom Snake, acting under the identity of Big Boss, saved them.

Behind the scenes
If Big Boss rescues Chico first, he will give Big Boss his cassette, which can give him a hint on where Paz is located. How he'll give Big Boss his cassette tape will also vary depending on the player's actions: If Big Boss put him down, a cutscene will play where Big Boss will inquire Paz's location, resulting in Chico supplying Big Boss with his Walkman with the tape playing sounds from Paz's torture before twice telling Big Boss that she had already been killed. If Big Boss put him onto the chopper, the tape will fall out via the ramp and land just as Big Boss is about to leave the premises and the chopper, causing him to reach down and pick it up.

If Big Boss is to rescue Paz first, and lies her down in the landing zone cave, he will notice her pained expression and place her into the recovery position, thereby negating the need for Chico's cassette tape. If this is the player's first playthrough, however, they will miss out on this cassette tape by rescuing Paz first.

If Big Boss rescues Chico first, then Paz and leaves them in the RV cave, Chico will lay down next to Paz, mumble her name, and try to talk to her in an attempt to apologize for what happened. Paz will, in turn, hum a song to try and comfort Chico.

On an audio tape which was recorded during the implementation-procedure of Paz' explosives, Skull Face heavily implies that the second bomb had been inserted into Paz' vagina.