In the first release of Pikmin, Captain Olimar lands on an uncharted planet. This planet gets reported to Olimar that it has high levels of oxygen which is toxic to his people that live on the planet Hocotate.
Throughout the series, you encounter many kinds of man-made objects, such as boxes, tin cans, and even a bottle stuck in a pond.
If that's not enough, Captain Olimar is ignorant to the use of a Geiger Counter due to "Not reading the manual". If you were a kid growing up with this game, you wouldn't know either, since it was never explained in the game what a Geiger Counter does.
What a Geiger Counter does is track levels of radiation in a given area. When you extract it from a Burrowing Snarget in the Forest of Hope, you can hear it buzzing and the needle constantly in action. Even when you return it to the S.S Dolphin, no matter where you go, the Geiger Counter is constantly going off. It seemingly serves to only annoy Captain Olimar, but it should have served as an indicator that the planet, in addition to having high levels of oxygen, has high levels of radiation all over the surface. If you look closely enough in the Distant Spring area, especially in the Perplexing Pool in Pikmin 2, you would see that it resembles the remnants of a bathroom. The hole that leads to the Shower Room area is actually a drain in the bathtub.
Throughout Pikmin 2, you are collecting treasure. The treasure you have been collecting have been origins of the culture of our civilisation. Most of the treasure you collect is underground. Throughout subterranean levels, you encounter more remnants of our past. You see a locket that contains a picture of a dog, dig up a skull, and you even obtain the head of a baby doll. In the Hole of Heroes whose underground area contains the most levels, piece by piece, you encounter R.O.B the Robot who's dubbed by the ship as, "Remembered Old Buddy".
In the Emergence Cave in the Valley of Repose, and in the Awakening Wood area, you find two parts that once formed the globe of our planet. These two parts were necessary to reach two different areas in the game.
When you get "The Key", the Ship informs you of an inter-dimensional message showing: "Challenge Mode can now be accessed from the title screen". However, the Ship fails to understand a single word of the message, dismissing it as gibberish and expressing hope that the message reached its intended recipient. Our English language appears to be completely untranslatable to the species residing in Hocotate.
Between Pikmin 2 and Pikmin 3, the planet was named PNF-404 by the inhabitants of Koppai in their search for food sources because of resource depletion, and the continents of our planet have changed drastically. The continental shape of the planet appears to be in the form of Pangea, the super-continent that was once our countries put together existing once in the late Paleozoic era and the early Mesozoic era.
Scientists in our age today have made a collective hypothesis: In two hundred fifty million years, Pangea will reform due to gradual tectonic plate movements. In fact, as we speak, the continents are slowly, very slowly, moving.
In Pikmin 3, the relics of our civilisation almost deteriorated. Nearly all of the remnants of our existence have been buried beneath the history that is the ground. Throughout the game, you see that the environment is made naturally, as opposed to being man-made by our hands that once existed.
However, long before the events of the games began, humanity found a sliver of hope to continue living on. On a distant area that has been previously ruined by radiation grew peculiar flowers. They were red, yellow, blue, purple, grey, and pink. Humanity was searching for some way to survive the impending nuclear apocalypse and live on in some way or another. After failing to perform DNA splicing on animals, they found these flowers.
Scientists found that these flowers were lively as they frequently closed their pedals so suddenly, as if trapping prey like a Venus Flytrap. In the centre of the flower, they decided to perform DNA splicing. When the flower closed its pedals, it ejected what appeared to be seeds. Scientists grew interested when the flower rotted afterward shortly after expelling its seeds, almost immediately.
They grew interested when they found that the seeds were swaying back and forth without the benefit of wind, with the leaf glowing light a nightlight. Even more interesting was that it only took five hours for the leaf to bloom into a flower.
When a scientist gently uprooted the plant after it bloomed to inspect its roots, they were greatly surprised. It turns out that it was a living creature. The scientists were astonished at what they saw. It had beady eyes, tiny arms and legs, and even a nose. This creature was red.
The scientists gently plucked more of these human-like plant creatures after performing some more DNA splicing and infusing the flowers. They studied their results.
As a whole, these creatures were lively. Collectively, they were quite a force to be reckoned with. Their strength was deceiving. When they were forced in certain scenarios, it was discovered that they had enough strength as a unit to tear down wooden barriers, construct bridges out of sticks, push movable objects, and lift objects to destinations.
The more they experimented with these creatures, the more interested the scientists became. They tested these creatures on their survival skills. They pitted them against predators and elemental hazards. Countless deaths of these creatures were reported, but the strengths of each creature was revealed with enough experimenting and breeding.
Their entries revealed the following:
Red- Fire resistant. Has a sharp nose. Seems to be more offensive-oriented than most types.
Yellow- Loves to charge itself with electricity, and takes no harm from it. Has large ears. Lightly weighted with extremely proficient jumping capabilities. Seems to have a passion for explosives for a mysterious reason...
Blue- Possesses a set of gills which allows them to freely swim in water. Seemingly able to survive in any water source.
White- Immune to poison. Swift and small in stature. Beady-red eyes that are able to detect solid matter underneath the ground. When chewed by predators, their poisonous bodily fluids deteriorate their predator's health, possibly killing them.
Purple- Heavyweight. Seem to possess a lax and calm nature. They do not seem to panic. it is so incredibly strong that its strength equals that of ten ordinary cousins. When attacking, it pounds itself on the enemy and can sometimes stun them. However, they don't seem to possess a resistance to any elements.
Rock- Infused with mineral corundums. Cannot be chewed or crushed, and is resistant to weak brute force. Can crash through solid glass, ice, crystal, even the hides of some predators.
Winged- Can fly over hazards but weak combat skills.
The most important thing they found out was that these plant-like creatures were immune to radiation when exposed to it. Eager, they bred these flowers and sought to increase the population. However, these creatures needed a name. Thus, the Pikmin were born.
Pikmin is derived from the words, "Pick" and "Man".
This remained a top-secret project, whose information was never released to the public.
The Pikmin, however, didn't seem to show signs of aging for unknown reasons. The Pikmin also didn't seem to display high intelligence, instead responding to stimuli much in the same way that a five year old child would.
Also, like real humans, the Pikmin cannot live in a natural habitat. The humans invented a device that would act as a mobile home, and an incubator that transforms nutrients from carcasses and the nectar to breed more Pikmin thanks to the programming the scientists made for it. Emergency functions were made for the mobile device to prevent extinction.
It took a while, but Pikmin came to recognise the mobile home as their habitat.
After the first successful one, the humans started to make more. Like the Pikmin, they were resistant to the elements, especially radiation. The Pikmin were stored in many replicas one by one, and when their homes detect a nearby light source at the right frequency, they'll activate and expel their seed to greet who discovered them. The Pikmin would be taken care of, humans hoped.
The nuclear apocalypse passed, and then millions of years later, the Pikmin were discovered by Captain Olimar, and thus, the series of the games began.
Even though the creator Shigeru Miyamoto addressed directly that the planet PNF-404 is in a state where humans are extinct, it is never outright stated that the PNF-404 is actually our planet.
His Pikmin series are a glimpse into our future, what our planet would look like in a million years from our time, and how we'll live on in plants, rocks, and puny flies, fighting for survival against the vicious creatures out to eat us. The Geiger Counter goes off constantly, implying radiation throughout the entire planet. The Pikmin series must have foreseen that we'd meet our end in a massive nuclear apocalypse. Then, creatures that survived the nuclear apocalypse will learn to coexist peacefully after we died out, and then alien species will discover our planet, see that the remnants of our civilisation holds high monetary value and sell them off to make money to pay off debts, and use our planet as a resource node to feed their own species.