Around the time of the original release of Pikmin, Producer Shigeru Miyamoto famously "said" that the Pikmin series takes place on planet Earth after the extinction of the human race. His exact words are difficult to trace and verify, which has caused some disbelief amongst the Nintendo community, but this sentiment is evidenced several times throughout the series by subtle hints left for us by the developers.
Beyond our knowledge that the atmosphere of the Pikmin's home world is comprised significantly of oxygen, in the original Pikmin, we see rusted cans, shattered flower pots, old cardboard boxes, and other various pieces of evidence that this world was once home to a society much like our own.
Pikmin 2 takes this idea much further—and does so much more blatantly—as Olimar revisits PNF–404 for some good old fashioned treasure hunting. These "treasures" he finds are products like Duracell batteries, Vlasic pickle lids, and Dr. Pepper bottle caps buried extremely deep underground. Also in Pikmin 2, Olimar retrieves two halves of a globe. On the "Spherical Atlas," as Olimar calls it, we can clearly see familiar land masses and country borders of the Northern Hemisphere—including the division of East and West Germany, meaning the globe was produced sometime before the German reunification in 1990. On the "Geographic Projection," we see the Southern Hemisphere and its familiar land masses, including Australia and South America. Pikmin 2’s last piece of evidence that PNF–404 is actually Earth comes form the closing cinematic of the game, where players get a full view of the planet. In this shot, players can clearly see land masses strikingly similar to Southeast Asia, Oceania, and Japan.
Now, all this proves that PNF–404 is indeed Earth, but until Pikmin 3, there was nothing truly supporting the idea that humans had gone extinct, as opposed to the idea that PNF–404 was simply a fictitious alternate version of the planet taking place in our own time. In Pikmin 3, three explorers from the planet Koppai crash land on PNF–404, whose geography has now been retconned to resemble Pangaea Ultima, a scientific hypothesis on the appearance of Earth in 250 million years.
*To the right you can see a little comparison chart I've cooked up. Above is a "rough estimate" of Pangaea Ultima. Below is PNF–404 in Pikmin 3.*
Due to the developers’ conscious decision to set the game on Pangaea Ultima, alongside the countless signs of the prehistoric existence of our very own, nonfictional civilization, we can finally piece together this puzzle and determine that PNF–404 is, in fact, a post-apocalyptic Earth... 250 million years in the future.
Thanks to Pikmin Wiki for providing the trivia necessary for this article.