The Nazis are the followers of the ideology of National Socialism, more commonly known as Nazism. Originally from Germany, they made minor appearances in Drake's Fortune and Among Thieves. In the first game, Nazi soldier corpses were first encountered in the Amazon, and then later again in the bunker on the hidden island. In Among Thieves, Nathan Drake also found evidence of a Nazi expedition to Shambhala, led by Karl Schäfer.
Prior to Drake's Fortune
At some point prior to, or during, World War II, Nazi Germany re-discovered an uncharted island in the Pacific Ocean. On the island they discovered a former Spanish colony, and decided to construct a bunker with a submarine dock. At some point during their constructions they discovered the treasure vault, the corpse of Sir Francis Drake, his map of the island, and El Dorado. They removed the golden sarcophagus and all other treasure from the vault, and at some point opened it in their bunker, which caused one of their soldiers to transform. They recorded him alongside the statue, the footage showing him breaking free of his restraints and charging the camera.
Afterwards they placed it in another cavern hidden underneath the graveyard in the monastery, leaving a detailed map of the cave and the hidden access tunnel in their bunker. At some point a submarine was also sent out to the Amazon jungle, headed for the original location of El Dorado. Presumably they knew of the location thanks to information taken from the island, as the diary containing all of Drake's details, except the torn-out last page, was hidden inside his fake coffin. Said submarine then got stranded deep inside the Amazon jungle. Sometime afterwards, before the end of the war, the Nazi soldiers on the island were all wiped out by the descendants.
Nathan Drake and Victor Sullivan first stumbled upon a stranded Nazi U-boat in the Amazon rainforest, close to an ancient temple, in "A Surprising Find". They deduced it must have come up the river during flood season, and subsequently gotten stuck. On-board Nate found a corpse with Spanish coins, stamped with an unknown mint mark. Shortly afterward he discovered the remains of the captain, which to his eyes seemed to have been killed by being torn to shreds. Presumably, this would have been done by an onboard captive descendant, possibly a Nazi soldier, who got loose and attacked the crew.
Nate also discovered that the captain had a map, which was the original final page from Francis Drake's diary, torn out by himself, which the Nazis must have taken from his corpse. The island design on the map corresponded with an official Nazi map, of an island named the 'Hidden island' ('Hidden Island'), with the coordinates UK2642. Nate used a Nazi coordinate chart to figure out the location of the island itself, taking Drake's map with him. Later, at the end of "The Heart of the Vault", Nate and Elena accidentally discovered an abandoned Nazi bunker, connected to the Spanish treasure vault. They found a Nazi map, which depicted the true location of El Dorado underneath the church.
While Nate turned on the bunker's power in "The Bunker", he was shortly after forced to fight dozens of descendants in "Unwelcome Guests", which appeared to have easy access to the entire bunker through large pipes. He used to Nazis MP40 machine gun to do so, which were littered throughout the base, indicating they died fighting. He also found a projector with short footage showing El Dorado, and a cursed Nazi soldier chained to a pillar, as well as Francis Drake's testament and final words.
Prior or during World War II, Karl Schäfer led a group of Nazis on an Ahnenerbe expedition to find the Cintamani Stone 70 years before the events of Among Thieves. After learning the truth about the Cintamani Stone, and after several of his men ate the resin from the Tree of Life. Schäfer shot and killed his entire expedition. He was severely wounded in the process and managed to make it to Tenzin's village, where he remained until Nathan Drake arrived 70 years later. Nazi corpses can be found still in the Himalayas with MP40s and P08-9mms.
Schäfer tries to convince Drake that the Cintamani Stone was real. As he still believes that the stone is just a myth, Schäfer told him to find the remnants of his expedition. Tenzin accompanies Drake after mountaineering in the Himalayas, they found a temple and were attacked by the Shambhala Guardians. Later, they found the last resting place of the Nazis.