Third Sun

Third Sun is set in an undisclosed, Eastern European town. Old Snake is dropped off there after Raiden tells him that he needs to meet up with an enigmatic member of a resistance movement against the growing threat of PMCs, and the very likely case of Liquid Ocelot having gone there himself. Snake, knowing that he has been blacklisted and will be killed on sight if he goes out into the public, wears a trenchcoat over his musclesuit and uses the FaceCamo acquired from Laughing Octopus to make himself appear much younger. He is almost discovered right off the bat when he refuses to pass through a PMC checkin station, going through which would instantly reveal who he really was thanks to nanomachine identification, before Meryl Silverburgh, acting as a leader of the PMCs as she works undercover for the government, appears and "arrests" Snake, taking him into the city. The two have a short conversation about Snake's motives before she becomes angered at his finality about having to kill Liquid, proclaiming him to be an idiotic old man before leaving.

Snake brushes off the altercation and initiates his mission, the objective being to find Big Mama. He and Otacon decide that, being that she is the leader of a resistance movement and thus most likely at the movement's HQ, the best course of action would be to follow a member of the Resistance back to the base, members being easily identifiable by the distinct tune they whistle as they try to nonchalantly pass through the streets.

Dodging around PMC soldiers patrolling the area for anyone breaking curfew, Snake successfully trails a member back to the base, where he easily infiltrates and disarms several of them before Big Mama appears and orders everyone to stand down. The members exit, leaving Snake and Big Mama to themselves.

Big Mama does not waste words, telling Snake that she is, in fact, his mother, the egg that was fertilized with Big Boss' DNA that would eventually become Snake planted in her uterus to grow into a child. But this is hardly the most shocking revelation she has for the aging soldier; She tells him that The Patriots, before becoming the tyrannical system of AIs that it was today, was comprised of only a few people: Major Zero, the founder, herself, under the codename EVA at that time, Revolver Ocelot, a doctor named Dr. Clark, otherwise known as Para-Medic, Donald Anderson AKA Sigint, and Big Boss. She explains that what would eventually evolve into the all-controlling shadowy computer systems of the day started as increading arguments between Big Boss and Zero, with Big Boss becoming increasingly worried and agitated over Zero's power control. The final straw came when Zero took Big Boss's cells while he was in a coma and started the Les Enfants Terribles project. After that, Big Boss left the group in disgust and began plans for what would become Outer Heaven. Zero, disillusioned, decided that, if his hero and idol would betray him like that, he couldn't trust anybody. Thus, he created the AIs that were in place today, though he had no idea at the time that they would become what they had.

Big Mama reveals another shocking truth - Big Boss wasn't dead. He was left severely injured, and his nanomachines locked his consciousness away leaving him in a vegetative state, but he was, in fact, alive. What's more - the resistance was in possession of his body. Keeping the pyx inside of a van where extensive life support was used to keep him medically alive, the unrecognizable, withered, blackened body said to be Big Boss lies, responding to sounds in a primal way.

One of the Resistance members informs Big Mama that PMC troopers are coming and will be on them in less than five minutes. She initiates the escape plan - three decoy vans would draw the PMC's attention while the real one took the direct escape route. Hopping aboard her motorcycle, Big Mama and Snake sped through the streets, being chased by another member of the Beauty and The Beast Unit, Raging Raven. After a long, drawn-out chase, Raging Raven destroyed the van carrying the body with a missile, also sending Big Mama and Snake flying, causing Big Mama to be impaled on a rebar pipe. Helping Big Mama inside a nearby building, Snake heads up the stairs and fights Raging Raven, ultimately defeating her. Like Laughing Octopus before her, Raven's armor falls off after she is beaten and she proclaims that she is not angry anymore, once again being put down by Snake before Drebin relates her tragic past as well. Snake takes her grenade launcher after her defeat and heads back down to Big Mama, who tells him that all of the vans were decoys, and the body was in fact waiting on a boat in the nearby river. Snake helps Big Mama as they make their way to the river, only to find Liquid waiting for them.

Liquid easily bests Snake in CQC combat, all the while preaching about destiny and about freeing themselves from the System. After responding to Big Mama's cry of "Adam!" by taking the apple she was holding and crushing it, Liquid gets on his own junk along with Vamp and, shockingly, Naomi Hunter, who appears to have defected back to Liquid's side, and prepares to leave, only to be stopped by Meryl and a very large score of soldiers who have surrounded them. Liquid laughs and demonstrates that, now that he has taken Big Boss' DNA, he has total control over the SOP System inside the soldiers' bodies. By merely pointing his fingers, he first takes away everyone's ability to fire their weapons, and then, with a simple cry of "Die!", causes many of them to start seizing up and having heart attacks. He controls his own army, the FROGS, who shoot and kill many of the soldiers, causing Meryl's boat to capsize and the boat Big Mama had reserved to use as an escape to catch fire. Liquid takes the body they had been transporting and throws it into the flames, proclaiming he doesn't need it anymore. Crazed, Big Mama runs into the fire to try and retrive the body. Snake pulls her out, burning the left side of his face badly in the process. Big Mama dies shortly thereafter.