Phantom Pain Incident

The Restoration of Mother Base and the hunt for Cipher were a series of missions that took place in Afghanistan and Central Africa in an attempt to build a new Mother Base to replace the one that was destroyed in Cipher's XOF Trojan Horse operation and to find out about Cipher's plans, hunt them down and exact revenge on the group that was responsible for the destruction of the original Mother Base and the unit before Diamond Dogs, Militaires Sans Frontières.

"Phantom Limbs"
After escaping from the hospital, Ocelot and Venom Snake arrived in Afghanistan to save Kazuhira Miller who was captured by Soviet soldiers while training Mujahideen. After familiarizing himself with his new equipment, Venom Snake infiltrated a Soviet-occupied village Da Wialo Kallai to learn Miller's whereabouts.

After finding out the exact location of Miller in Da Ghwandai Khar, Venom Snake saved his old comrade and carried him to the extraction point only to find out that the helicopter couldn't land because of the sudden mist. Moments later, Venom Snake and Miller were ambushed by the mist squad of the Parasite Unit. After dealing with the Parasite Unit, Snake brought Miller onto the helicopter.

"Diamond Dogs"
When Venom Snake and Miller arrived on the Command Center of Mother Base, they were greeted by Ocelot and Diamond Dogs members who took Miller to a medical facility on the base. Before he was carried away, however, Miller and Venom Snake pledged to exact revenge on Cipher and decided to start by doing wet work in Afghanistan to find some clues as to where Cipher might be.

Venom Snake accepted the role of the leader of Diamond Dogs, familiarized himself with the new Mother Base and moved on to his next mission.

"A Hero's Way"
Venom Snake accepted a mission from the CIA. They wanted a a prominent Spetsnaz commander dead. Miller recommended that a soldier of his caliber would be useful to Diamond Dogs. The CIA had heard rumors of his involvement with the disappearance of the Hamid fighters in Da Smasei Laman and decided he was a dangerous enemy. Venom Snake inflitrated Da Shago Kallai outpost where the commander was stationed. While interrogating the commander, Venom Snake learned that the Soviets weren't actually involved with the incident in Da Smasei Laman and that the region was controlled by an unknown force.

"C2W"
In order to make operations in Afghanistan easier, Miller decided that Venom Snake should infiltrate Eastern Communications Post and destroy comms equipment there to put a hole in the Soviet base-to-base comms network. Venom Snake successfully carried out the mission.

"Over the Fence"
Miller learned that the Soviet bionics engineer responsible for creating Venom Snake's arm was captured by the Soviets and brought to Wakh Sind Barracks as a prisoner after a failed attempt to defect. Miller asked Venom Snake to rescue the prisoner. Venom Snake infiltrated Wakh Sind Barracks and saved the engineer, who became a part of the R&D department of Diamond Dogs and continued his work on the prosthetic hand, modifying it for Venom Snake.

"Where Do the Bees Sleep?"
Venom Snake accepted one more mission from the CIA related to the disappearance of the Hamid fighters in Da Smasei Laman. The CIA had been supplying the mujahideen with a new type of rocket launcher called Honey Bee. When those mujahideen disappeared from the fort, the CIA was afraid the Soviets would move in and secure the weapon. Venom Snakr was to infiltrate Da Smasei and to extract that weapon before the Soviets could find it. On his way to the fort, Venom Snake enountered a mute Hamid prisoner, the only survivor from Da Smasei.

He was escorted by Soviet soldiers who wanted the prisoner to show them the way to the Honey Bee. Venom Snake saved the prisoner and got the directions to the cave in Da Smasei where the weapon was hidden. The prisoner was extracted and recieved codename Silent Basilisk upon recruitment into Diamond Dogs. Venom Snake followed the directions recieved from the prisoner and found the Honey Bee in the caves in Da Smasei.

When he tried to escape the fort, he was ambushed by Skull Face. Skull Face grabbed Snake with with a mechanical arm and intimidated him, saying that this time he should "rest in peace." When Metal Gear Sahelanthropus released Venom Snake, he found himself surrounded by the mist squad of the Parasite Unit, who have turned all Soviet soldiers in the base into their puppets. He eventually left the area with the Honey Bee.

"Red Brass"
As Venom Snake was getting more involved in Afghanistan, his activities were noticed by three Soviet commanders - Wialo Company commander, Shago Platoon commander and Wakh Sind Platoon commander. They arranged to meet in Da Wialo Kallai to discuss how they should deal with this new threat. A rebel guerilla faction in Afghanistan learned of that plan and hired Venom Snake to eliminate the commanders during the meeting. Snake would infiltrate Da Wialo Kallai.

"Occupation Forces"
After the soldiers in Da Smasei Laman were turned into puppets by the Parasite Unit, Soviets didn't give up on taking the fortress under their control. They've sent new troops to Da Smasei and were planning to reinforce them with a lieutenant colonel from Qarya Sakhra Ee and his tank column. Venom Snake recieved a mission to stop these forces from deploying at Da Smasei. He first infiltrated Qarya Sakhra Ee to learn the time of the deployment and the path the reinforcements were taking and then intercepted the column.

"Backup, Back Down"
The rebel forces in Afghanistan were planning a major offensive against the Soviets and they've hired Venom Snake to destroy enemy reinforcements that would be moving in during the offensive. Venom Snake completed the mission.

"Traitors' Caravan"
Venom Snake is tasked with extracting a truck of supposed high importance, seeking proof that Cipher is behind the events unfolding. Tracking the truck's transfer throughout Central Africa, Snake watches in shock as, when he nears the truck, the Skulls explode out of the truck's back, proving Cipher is involved. Snake manages to eliminate the Parasite Unit once again and successfully gets the truck extracted for investigation.

"Voices"
Intel reveals an escaped child soldier named Shabani is being held at an industrial zone in Central Africa known as the Devil's House, and after sneaking through several outposts and enemy patrols, Snake manages to infiltrate the long abandoned factory. Snake finds several wards, filled with people on beds, with earbuds gouged into their throats playing sound out of a tape and disgusting growths on their chests. After trudging his way through this horrific scene, Snake eventually finds Shabani, experimentally tortured all the same as everyone else, but before he can rescue him, looks into the other room via a medical curtain to see none other than Skull Face himself executing one of his victims.

Shabani's pained cries and pleas for death alerts Skull Face, and upon spotting Snake, orders The Third Boy to finish him off. The boy does this by summoning The Man on Fire, who already has the upper hand and begins strangling Snake. Fortunately, The Man on Fire is temporarily disabled, allowing Snake to escape, as pieces of the boy's true personality leaks out and he uses his mental power to mercy-kill Shabani instead of power Volgin. The boy is then influenced by the man's rage yet again and the entire factory goes up in flames. After Snake's one escape is blocked off, he is forced to fight the Man on Fire, eventually incapacitating him for a few moments where he uses this window to escape via a chopper.

"Code Talker"
After some intel reveals an elderly man named Code Talker who researched the vocal cord parasites and was forced to work for Skull Face is being held captive at a mansion in Central Africa, Snake is sent to rescue him. On his way there, a thick blanket of mist soon rolls in and the Skulls appear, but this time it's a different unit of female snipers, still possessing the superhuman abilities of the original unit.

Snake is forced to either fight the Skulls or flee from the barrages of sniper fire into the jungle, where he eventually resurfaces at the heavily guarded mansion, breaks into the basement, and finds Code Talker. After getting out of the mansion with Code Talker slung over his back, if Snake fled from the Skulls, he realizes the mist of the jungle consumed the mansion, and the place is now flooded with zombie-fied soldiers. However, if Snake had neutralized the Skulls, the soldiers stayed normal and the road leading to landing zone was blocked by an armored vehicle and few patrolling soldiers. Snake manages to evade both them and, if the Skulls aren't eliminated, the sniper fire of the Skulls, and makes his way to the chopper. However, the mist consumes the helicopter as well, causing the windows to explode, killing Pequod in a barrage of jagged glass and causing the chopper to crash.

"Metallic Archaea"
The ravaged chopper crashed in the Nova Braga Airport, where Snake and the unconscious Code Talker fortunately survived. However, as Snake crawls out of the wreckage, he realizes he is surrounded by the Skulls, and the mist makes it so calling another chopper is impossible, forcing him to fight and permanently kill them once and for all. After a grueling battle, the mist clears and Code Talker and Snake are picked up by another chopper. The aftermath of these events has Code Talker recruited into Mother Base as a scientist, where he reveals almost everything about the parasites such as their properties.

"Skull Face"
With the intent to capture and interrogate Skull Face, Venom Snake infiltrates his heavily guarded fortress and confronts him on a helipad. Outnumbered by a squad of XOF soldiers, Snake is forced to surrender and follow Skull Face, who explained along the way to the jeeps that he has known Snake since 1964 Soviet territory and Zero's plans During the ride throughout the roads of Afghanistan on a jeep with Skull Face, he passionately explains his plans; worldwide ethnic cleansing with the parasites, and the reasons behind them; both his hated for Zero and his broken childhood where he was heartlessly stripped of his culture.

The XOF transport parks at the Serak Power Plant, the lair of the dormant Sahelanthropus, almost ready for activation. Skull Face has The Man on Fire manifest to finish Venom Snake off, but The Third Boy donates his telepathic power to Eli and his vicious hatred against Snake instead of The Man on Fire's hatred, as Miller, Huey, and Eli are in a helicopter surveying the events unfolding. The Third Boy has The Man on Fire apparently commit suicide to get rid of him and he and Eli use their combined mental power to prematurely activate Sahelanthropus, leaving Skull Face defeated and shocked. XOF opens fire on the Metal Gear as they retreat, but it quickly slaughters them, and the mission ends with the wild Salelanthropus roaring in Venom Snake's face.

"Sahelanthropus"
Immediately afterwards, Venom Snake as well as the forces of XOF and Skull Face flee the power plant. Sahalanthropus relentlessly chases Venom Snake through a valley, and after realizing it can't fit, evolves from its hunched-over stance into a towering stand before resuming its attack on XOF. Despite barrages of gun-fire and tank rounds, Sahalanthropus absorbs it all, and easily destroys every last unit of XOF, leaving only Skull Face. The commander is surrounded by a circle of flames, and with the parasite capsule in his hands, begins narrating to Zero spiritually that even though he knows Cipher will wipe Skull Face from existence, he and his fiery vengeance will still make their marks in history through the might of Sahelanthropus, immediately before getting crushed by it. Meanwhile, Venom Snake, who witnessed this massacre in hiding, hijacks a surviving military jeep and attempts to outrun Sahelanthropus, who is in intense pursuit.

The war-machine's attacks eventually drive Snake off the road after being informed by Miller that destroying it is a necessity, as the world's knowledge of it would cause irrevocable chaos. After a lengthy battle, Snake manages to incapacitate the mechanical beast. Miller's chopper lands and picks up Snake, before flying over to Skull Face's mangled, debris-crushed body for some long awaited revenge. Snake destroys the parasite capsules by tossing them in a fire, but The Third Boy manages to salvage the last one, unbeknownst to anyone else. Using Skull Face's own shotgun, the two blow off his limbs as payback, and with one final "Mission complete" from Miller to Snake, the two leave Skull Face to die in horrible agony. However, Huey ultimately finishes him off, happily declaring "Revenge!" and they all return to Mother Base where they house Sahelanthropus's battle-damaged corpse, where Snake sees a phantom of the deceased Skull Face, with Kaz stating that even with Skull Face dead, the Phantom Pain remains.