The Nazis were 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 island. In Among Thieves, Nathan Drake also found evidence of a Nazi expedition to Shambhala, led by Karl Schäfer.
Nathan Drake and Victor Sullivan first stumbled upon a stranded German 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, and which somehow made it into the hands of the Nazis. The island design on the map corresponded with an official Nazi map, with an island named the 'Versteckte Insel' ('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. It remains unclear as to why the U-boat specifically made it this deep into the Amazon since they had already found El Dorado.
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 of the monastery, which depicted the true location of El Dorado, indicating the Nazis had broken into the vault, emptied it, and moved the contents to a second hidden location.
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. Nate afterwards exited the bunker, making his way through more descendants and Atoq Navarro's mercenaries.