About a decade passes. Big Boss-as both Venom and himself-becomes even more of a legend. At some point, he returns to lead FOXHOUND, while developing Outer Heaven in South Africa with Venom. He also became a benefactor to the war-orphaned girls who would grow up to be Naomi Hunter and Sniper Wolf; and a friend of Frank Jaeger (Who possibly knew him as far as the San Hierenymo inccident). While Big Boss was publicly leading Foxhound, the identity of the leader of Outer Heaven remained a mystery.
During his leadership of FOXHOUND, Big Boss came across his cloned son, David, who was a rookie in the unit (Venom had an encounter with Eli, his brother, earlier on). At some point, Big Boss commissioned development of a new Metal Gear-the TX-55-which could hold two nuclear weapons, although it was smaller and squatter than it’s predecessors. He captured the scientist Dr. Madnar and his family to develop the device.
Eventually, Metal Gear neared completion. A member of FOXHOUND-Frank Jaeger-code named Gray Fox-was sent into Outer Heaven to investigate. Before he was captured, he sent of a transmission warning of the Metal Gear.
In his capacity as FOXHOUND leader, Big Boss sent David-now codenamed Solid Snake-into Outer Heaven, hoping he would fail the mission or give false intel. However, Solid Snake performed above Big Boss’s expectations, rescuing Fox and destroying the Metal Gear before it could be deployed as well. In an attempt to make him fail, Big Boss started to give him false information and orders, such as to abandon the mission. But Solid Snake pressed on, and then confronted the leader of Outer Heaven, Big Boss’s “phantom” Venom Snake, and killed him.
After the defeat of Big Boss and destruction of the main Outer Heaven fortress, the county itself was destroyed in multiple air strikes (possibly ordered by the Patriots who still viewed Big Boss as an enemy, and his outer heaven counter to their world order), killing a large number of it’s civilian population, as well as those who had rebelled against Big Boss. However, Big Boss managed to evacuate many, who then devoted themselves to him. He also swore he’d meet Solid Snake again.
Presumed dead, Big Boss built up “Zanzibar Land”, possibly close to Tselinoyarsk…in a way, Big Boss had become like Volgin before him-a warmonger with a deadly nuclear weapon. With Madnar, Grey Fox, and former rebel leader Schneider now serving under him, he commissioned the development of a new Metal Gear-Metal Gear D. In order to create further conflict, he kidnapped the developer of a revolutionary algae called OILIX (in an attempt perhaps at a monopoly), and raided several nuclear sites using the fully operational Metal gear-to give Zanzibar band a leg up in nuclear power-and presumabely as ammo for D.
FOXHOUND-now led by Colonel Campbell-brought Solid Snake out of retirement, and sent him to Zanzibar land where he quickly learned the truth-and also was shocked about the loyalty of his former comrades to Big Boss. Nevertheless, he destroyed the new Metal Gear, and then finally confronted Big Boss, who outlined his somewhat more twisted vision of a nation for soldiers-but also a world in perpetual conflict so those soldiers would always be needed. He also revealed that he was Solid Snake’s father.
Snake-who had lost most of his equipment during the battle with the Metal Gear-was able to improvise a flamethrower with just a lighter and aerosol.
Seems familiar, doesn’t it? Plus this was a snake he was killing, to boot.
This left Big Boss heavily injured but still somewhat alive. Once again in a coma, the Patriots identified his “soldier genes” and used them to treat some soldiers to give them abilities similar to this, the “Next Generation Special Forces”, or Genome army. However, this caused unfortunate side effects, such as mutations. When he took over Shadow Moses, Liquid Snake wanted to procure the body of his father to help cure the mutations of the army, who were brainwashed or served Liquid willingly.
Big Boss’s body however-it’s DNA code, to be precise-also held another secret, a way to access the Patriot’s mainframe (The Patriots themselves had gained far greater control at this point, and had created a “War Economy” somewhat similar to Big Boss’s own vision) His body was eventually recovered by his former lover Eva thanks to the help of Raiden, and she managed to repair it in part using Liquid and Solidus’s body. The remaining parts of Solidus remained useful however-the DNA of Solidus was pretty much identical to Big Boss (although it was still a fast aging Clone) and could be used to access the system just as easily. It also served as another decoy-and once Liquid Ocelot was able to use it to access the Sons of the Patiots system, he destroyed it…and everyone assumed that Big Boss was dead for good.
But when Solid Snake finally defeated the Patriots AI, Big Boss was revived, and able to finally find Patriots leader Zero, now in a vegatative state, his location a secret hidden using the AIs. He took Zero with him to Arlington cemetery, where he met Solid Snake/David….not to fight, but to explain how this whole mess with the Patriots started, that he and Zero had been wrong about the boss’s will…that it meant not a world of perpetual war or a world of information control, but to respect the will of others and one’s self.
Standing in front of her tombstone, he once again saluted, as he had fifty years before.
He also ended the life of Zero as well, cutting off his life support and choking him, ending the Patriots. However, he quickly got the FOXDIE virus from Solid Snake, which had been used to target specific enemies of the Patriots (But, to Solid Snake’s relief would not become a non-specific epidemic as he feared). As he lay dying, he shared one final smoke with his son, and told him to spend his remaining months not as a Snake, wasting his life fighting, but a man.
“This is good, isn’t it?”-he says, and Big Boss-hero, villain, legend-passed.