In 1997, he took control of another nation known as Zanzibar Land. Recruiting war orphans from across the Third World and raising them as soldiers, Big Boss hoped to create a nation by and for soldiers, where soldiers were honored and not treated as tools. Big Boss also recruited Gray Fox to his cause. To ensure Zanzibar Land's success, Big Boss once again commissioned the creation of a more advanced Metal Gear prototype, known as Metal Gear D. This time, Dr. Madnar developed the new model on his own free will, after being institutionalized into an asylum in the US. It is rumored that Dr. Madnar also provided Big Boss with cybernetic body parts to compensate for the injuries he received in Outer Heaven.
In 1999, Solid Snake once again managed to infiltrate the enemy nation and destroy Metal Gear. Snake eventually defeated Gray Fox hand-to-hand in the middle of a minefield. Bruised and unarmed, Snake was once again confronted by a machine gun-wielding Big Boss. Having spent his entire life on the battlefield, Big Boss could not conceive of a world without war. Big Boss paraphrased his mentor's final challenge to Snake before challenging his son to one final battle.
Snake managed to cobble together a makeshift flamethrower, using a can of lacquer spray and a cigarette lighter and used it to incinerate Big Boss.
Big Boss's body was recovered by the U.S. government and they discovered that he was, in fact, alive. He was injected with nanomachines to induce a sort of eternal coma. For Zero, Big Boss was an irreplaceable icon and, more importantly, an irreplaceable friend. Big Boss's genome was then used to identify the "soldier genes", which the U.S. government gave to the Next Generation Special Forces via gene therapy.