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Biology

The onions (so named because Olimar saw a resemblance between them and the onions of his planet)  act as both the nests of the Pikmin and their means of reproduction. They all have three thin legs covered with tiny hairs, a bulbous main section with a pattern across the side and a flower on top. Each onion can carry over a thousand Pikmin and Pikmin enter and exit the onion by using the openings at the top of the legs and can easily climb up or slide down the legs of the onion. Pikmin reproduce by bringing organic matter such as pellets or dead animals to the onion, which the onion will then suck up through a beam which shines out of its underside. After this, if there are fewer than 100 Pikmin in the surrounding area, Pikmin seeds will be dispersed from the center of the flower and will plant themselves in the earth around the onion. If there are 100 or more Pikmin in the surrounding area the onion will only begin releasing seeds after the number drops to under 100. The more organic matter is brought to the onion, the more seeds it will produce and if a pellet the same color as the onion is brought to it, it will also produce more seeds than usual. In the event of the extinction of a single species of Pikmin, the onion will release a single Pikmin seed on the day after the extinction. Each onion however will only produce seeds and act as a nest for Pikmin of the corresponding color. 
 
During the night the onion will fold its legs inwards and use the flower on top as a propeller to lift off of the ground. The onion will then stay hovering over the planet to protect Pikmin from nocturnal predators until daybreak. Onions also seem to have surprisingly strong level of responsiveness to the world around them, even following the protagonists rockets around the planet in the games. As Pikmin seem to be able to survive without consuming any kind of food or drink it has been hypothesized that the onion acts as a source of nutrition for the Pikmin. It has also been observed than onions can go into a type of hibernation where they turn a dark color, have their legs planted in the ground and do not have their flowers protruding. It's been theorized that this hibernation is a compensation for food shortages and that when conditions improve the onions will naturally come out of their dormant state. It is worth noting that Olimar managed to immediately awake three onions from hibernation simply by walking over to them though.
 
Despite there being five colors of Pikmin, onions only exist for the red, yellow and blue species of Pikmin. This means that either purple, white and Bulbmin onions have not been discovered yet or do not exist. It is also worth noting that in the ending of the original Pikmin, when Olimar and the S.S. Dolphin leave the planet, previously unseen onions of fourteen different colors can be seen flying after his ship, however these other colors of onions are neither seen or ever mentioned again. Only one of each color of onion has been seen so it is either than onions are very rare or that each specie of Pikmin actually only has a single onion.
 

Appearances

Pikmin

The onions first appear in the original Pikmin in their hibernating state. Olimar first finds the red onion and brings it out of its hibernation and then goes on to find the yellow onion and later the blue onion. As Olimar brings each one out of hibernation it produces a single seed for the Pikmin of its species. Olimar is able to call Pikmin out of the onions or send them back in and the onions will follow Olimar's ship around, allowing the Pikmin to aid him throughout the game. When Olimar leaves the planet at the end of the game he leaves the onions behind but a whole group of different colored onions are seen flying up, away from the planet. 
 

Pikmin 2

When Olimar returns to the planet with Louie in Pikmin 2 the onions are found in the same order, throughout different areas of the planet but are not found hibernating like in the first game. This is most likely a sign of the adaptation of the Pikmin to better survive in their environment, due to Olimar teaching them survival techniques in the first game. However, like in the first game when found the onions each disperse a single Pikmin seed, can be used to call or store Pikmin and follow Olimar's (and Louie's) rocket around the planet throughout the game.
 

Super Smash Bros. Brawl

In Super Smash Bros. Brawl onions will sometimes hover down from the air and land on the leaves on the 'Distant Planet' stage. Throwing pellets into the onions will cause them to produce items and throwing a pellet into an onion of the same color will cause additional items to be released. An onion trophy also exists in the game which includes all three of the onions on it.

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