Canon is any information that is considered to be "real", "official", or "true" in a fictional universe. For the most part, it is trivial to understand what constitutes as canon and what doesn't, as one needs to simply follow the storyline of a main Pikmin game. But there are some aspects outside of the story modes that could count as either canon or not.
Pure canon is all information that is undoubtedly canon; events that "really happened" in the Pikmin universe. This is mostly decided by the parties that develop the games and media related to the Pikmin franchise, meaning Nintendo EAD and Shigeru Miyamoto.
Currently, the story modes of the main Pikmin games – Pikmin, Pikmin 2 and Pikmin 3 – are considered canon. Hey! Pikmin is a spin-off game due to being a different genre and using some different mechanics from the main games, but since the story doesn't contradict the other games besides some small inconsistencies, Hey! Pikmin is generally considered canon. Bonus content, such as the reward obtained by completing all Pikmin 2 Challenge Mode levels with a pink flower, can vary in canon, but whenever it does not contradict with – and makes sense within the context of – the main story mode, it is considered canon.
Some content in some games could be considered canon or not. This could be because there is not enough information to accept or reject it as "real", or it could simply be a matter of opinion.
Trophies, stickers, and other side content in the Super Smash Bros. series feature canonical information from various games and often add extra information as well. For the most part, this extra information is created and approved by Nintendo, but its position in a non-canonical piece of media makes its status ambiguous. There have also been times where things like trophy descriptions contain information that directly contradicts the canon in the games. (For a list of such cases, see Mistake.) In general, though, anything said in these games can be considered canon, unless contradicted by a higher-priority source.
Some external content like the e-cards or the Pikmin Short Movies have information that matches up with the existing canon and makes sense in the Pikmin universe. However, no official word has been given on their canon, and because they do not belong to the main Pikmin series of games, their content is left as ambiguously canonical.
The amiibo compatibility in Hey! Pikmin is generally considered canon, assuming that Nintendo is believed to have existed inside the Pikmin universe. However, the Olimar and Pikmin amiibo existing in the game world sprout some paradoxes and overall don't make sense, so it's unlikely this feature is actually canon.
Pikmin 3 Deluxe's Side Stories mode gives Olimar's perspective before, during, and after the events of Pikmin 3's canon Story Mode. Olimar's Assignment, the first of these side stories, overlaps in time with Story Mode, as Olimar describes finding the cosmic-drive key at the end of the second day. In addition, the fact that the Distant Tundra is visited after the Twilight River means that for it to make sense, the Koppaites could not have cleared the first part of the Garden of Hope story in one day. While the events do line up with what's said in Olimar's data files from the Story Mode, the locations in Side Story missions are drastically different from the Story Mode versions, much like in Mission Mode. So while the story events in Side Stories could be considered canonical to the main story, the map alterations, signposts blocking off locations, and possibly the use of SPEROs are likely non-canon. However, it can be thought that the signposts and barriers simply represent the limits of what Olimar and Louie explore and that the SPEROs could simply be placeholders for some other device used to collect items.
Olimar's Comeback, the second of the Side Stories, further complicates this, as at the start of the Side Story, Louie is with Olimar. Pikmin 3 has four voyage logs that can apply to the final day depending on how much fruit is collected, and in two of these, it's heavily implied that Louie was left on the planet, meaning he couldn't be with Olimar at the start of Olimar's Comeback. Whether this means that Olimar's Comeback is non-canonical, or Olimar's Comeback only occurs if the Koppaites get specific numbers of fruits, or whether this is a mistake, is unknown, further complicating the canon.
Prima Games is a company that makes official strategy guides for various games, including Pikmin. On top of containing walkthroughs and tips, some guides include some extra information about aspects of a franchise; in the Pikmin series' case, this could be extra descriptions of enemies, for instance. It's clear that these guides are produced in collaboration with the developers, seeing that their guides usually contain maps and charts that were rendered using 3D models or in-game images, but in some cases, the extra information presented in the guides is not backed up by the canon game, and there have been times where the guides have contained incorrect information, like the time requirements for all of the Defeat Bosses! missions, or the wrong scientific name for the Breadbug. Regardless, Prima Guides are deemed official by Nintendo.
Some aspects in the games are not canon whatsoever. They belong to the game, but are considered to "not have happened" in the Pikmin universe.
The Super Smash Bros. series feature games that are considered non-canon for the franchises that take place in them. This is clear due to the fact that, naturally, Pikmin does not share a universe with the likes of Mario or The Legend of Zelda. It is also implied multiple times throughout the Super Smash Bros. series that the fighters are not their original characters, but rather toys brought to life by Master Hand.
Pikmin Adventure, despite being directly related to the Pikmin franchise, is not canon. It does not, in any way, relate to PNF-404 or the actual Pikmin, but rather, it is an attraction in the Nintendo Land theme park, themed around the Pikmin franchise.
Pikmin Bloom is not canon, due to having no connection to the story or characters of the other Pikmin games.
Activities that happen on an alternative game mode in a Pikmin game are not considered canon. Said game modes were created for the purpose of entertaining the player, and for the most part, they do not follow the main Story Mode's canon. For instance, it is canon that Captain Olimar landed on PNF-404 and had to gather his missing ship parts, not that he chose to begin a challenge where he had to cultivate the most Pikmin possible in one day.
Unused content, prerelease information, mistakes, sequence breaks, and glitches are not canon. They are content that the game developers did not intend to provide to the players in a finalized game, and should not count as such for the purpose of deciding the canon.
Some media, like movies, have a specifically defined canon, in which what happens in the movie is objective truth in the movie's universe, and cannot be altered. Games, however, vary according to each player's experience, so some aspects of the gameplay cannot be correctly considered canon or non-canon.
For instance, it is no truer that "Captain Olimar first recovered the UV Lamp and then the Massage Machine" as it is the other way around. For this, common sense dictates that varying truths are not accounted for in the lore. Following the previous example, it is canon that Captain Olimar recovered his ship parts, but their order of collection is not confirmed. There are times where such events are confirmed in a different game, however, normally in the form of a leader outright saying it (e.g. in his notes in Pikmin 2). Naturally, this does not change what a player might have actually done in their playthrough, but it does define the "standard", canon-wise.
The ending obtained in a game is also not relevant to the decision of the canon. Rather, the events that unfold in a following game decide which ending is the canon one.
So far, only two Pikmin games have multiple endings.
There are three endings in Pikmin, depending on how many ship parts the player collected and whether the player recovered the 25 mandatory parts. The canon ending is the "good" ending, where Captain Olimar successfully recovers all 30 ship parts. Evidence for this is in Pikmin 2, where Olimar has brought a souvenir home for his son, something that only likely happened after the collection of the Secret Safe, which is even implied by Olimar himself. In addition, it's revealed that Olimar's wife eventually finds a "secret cash stash", which can be assumed to be the Secret Safe. The ship's appearance in Pikmin 2 also supports this, as the antenna on the top of the Dolphin isn't bent and the lights on the sides are purple, which is only possible if Olimar collected the Secret Safe. The manual for Pikmin 2 also confirms that Captain Olimar did succeed in completely repairing the S.S. Dolphin.
There are four endings in Pikmin 3, and a game over state, depending on how much fruit the player obtains and if they ran out of juice or not, as explained here. At this point, none of the endings have been confirmed or denied to be canon. However, Olimar's Comeback complicates this, as Louie and Captain Olimar are together at the beginning of the Side Story. Two of the voyage logs on the final day imply that Louie was left behind on the planet. If these voyage logs are trusted, this could imply that either Olimar's Comeback is not canon, or these two endings are not canon.
Overview of the canon
While on an interstellar vacation, Captain Olimar switches his ship, the S.S. Dolphin, to autopilot and stands up from the control seat to make a cup of tea. He fails to notice a meteor, which hits the S.S. Dolphin and sends it plummeting to the surface of a nearby planet. During the chaos, Olimar was thrown against the control panel, and blacked out. He awakens on the surface of the planet, and discovers that 30 of the Dolphin's ship parts were scattered around the planet. Olimar's space suit's sensors then indicate that the atmosphere of the planet contains oxygen, which is extremely poisonous to Hocotatians. Fortunately, the life-support system built into his suit was unharmed, but the remaining battery power would only last him for 30 days. After exploring the area, Olimar finds a dormant Onion. When Olimar approaches the Onion, it seems to awaken, and spits out a seed. Olimar plucks the seed, discovers Red Pikmin, and utilizes their abilities to get back the Main Engine, which allows him to pilot the S.S. Dolphin once again. During his expedition on the planet, Olimar comes across Yellow Pikmin and Blue Pikmin, in that order. He finally manages to retrieve all of his missing ship parts, and grabs a "shiny alien platter" as a souvenir for his kid, before blasting off back to Hocotate.
When Olimar returns to Hocotate, he finds that the company he works for had to take out a loan to repay the loss of a cargo of golden Pikpik brand carrots. Louie reported that a ravenous space bunny ate the shipment, but they were actually eaten by Louie himself, as he couldn't suppress his powerful hunger. The president explains their situation to Olimar, who learns that the S.S. Dolphin was sold to help repay the loan. The remaining loan is revealed to be 10,100 Pokos and, in shock, Olimar accidentally drops the "alien platter" souvenir on the ground. As the souvenir rolled into Louie, the Hocotate ship was able to suck it up. It analyzed the piece of treasure to be worth 100 Pokos, which lowered the remaining loan to 10,000 Pokos. As a result, the President sends Olimar and Louie back to the planet to collect more treasure in hopes of paying off their debt.
While landing, they fly through a small blizzard in the Valley of Repose, and try to maneuver through some tree branches. Unfortunately, Olimar hits one of the branches, and Louie falls out of his cockpit, into the snow below. The Hocotate ship barely manages to land, and ejects Olimar out of his cockpit. He gets up and rediscovers Red Pikmin. After a while, the duo are able to reunite and salvage a piece of treasure. During their search for treasure the following days, Olimar and crew discover Purple Pikmin and White Pikmin, and rediscover Yellow Pikmin and Blue Pikmin, in that order. Eventually, they collect enough treasure to repay the debt and return to Hocotate, but during the trip back to their home planet, Louie gets left behind. After arriving at Hocotate Freight and emptying the Hocotate ship of all its treasure, Olimar informs the president that there is more treasure left on the planet. The president then orders Olimar and Louie to go back to the planet, but then realizes that Louie was actually left behind. The president decides to join Captain Olimar, and the two return to the strange planet. They recover Louie from the Titan Dweevil, and after collecting the rest of the treasure on the planet, they finally go back to Hocotate.
Some time after this, the planet of Koppai is in the midst of a planet-wide food crisis. They decide to send unmanned scout vessels, called SPEROs, out into space to search for planets that contain edible matter. The final SPERO returns with data indicating that one planet has "unlimited food resources". Koppai names the mysterious planet "PNF-404", and proceeds to send three explorers to PNF-404 in search of food. Unbeknownst to them however, Olimar and Louie also return to the planet to collect more treasure, as Hocotate Freight's new business venture failed miserably and the company has fallen into debt once again. Olimar and Louie start their search for treasure in Flower Garden. The next day they go to Inside Forest, but at the same time, the Koppaites' ship, the S.S. Drake, mysteriously fails, ejecting the Koppaites into different areas. Captain Charlie wakes up in the Distant Tundra, finds Yellow Pikmin, and eventually loses them when he's confronted with the Vehemoth Phosbat. Alph then wakes up to find himself in the Tropical Wilds, encounters Red Pikmin, and reunites with the S.S. Drake. He then learns that they cannot return to their home planet without the cosmic-drive key, which is nowhere to be found on the S.S. Drake. On the same day, during the start of Olimar and Louie's expedition in Inside Forest, the two come across the cosmic-drive key, which Olimar takes as a souvenir for his son.
Olimar and Louie head to River, and Olimar realizes that a number of his logs and notes have gone missing. Olimar also buries the Scorch Guard here, along with a log, as he states that he doesn't need it anymore. Meanwhile, Alph makes his way to the Garden of Hope, where he gets Rock Pikmin and reunites with Brittany. Before they begin their expedition in Tundra, Olimar finds Charlie's impact site and leaves the Anti-Electrifier with a note, due to the area having "many electrical contraptions". After defeating the Armored Mawdad, Alph expands the S.S. Drake's range using the Data Glutton, and Alph and Brittany discover the Distant Tundra. While landing in the Distant Tundra, Brittany gets knocked out of the ship and falls in a cave where she discovers Yellow Pikmin. Olimar and Louie finally collect enough treasure to repay their new debt, but Olimar picks up a reading of a golden object in the Formidable Oak. He ignores Louie's warnings about the area, and they go to the Formidable Oak the next day. While Olimar records his log, he gets captured by the Plasm Wraith, and Louie runs away. Olimar attempts to escape the area several times, but the Plasm Wraith repeatedly knocks him unconscious, since his spacesuit puts him in forced-sleep. During his escape, Louie is somehow ejected into Twilight River while the ship itself crash-lands in the Garden of Hope, losing several of its parts in the process.
Meanwhile, Alph and Brittany reunite once more in the Distant Tundra, take down the Vehemoth Phosbat, and rescue Charlie. They then track down a signal coming from the Tropical Wilds, and after defeating the Sandbelching Meerslug, Alph expands the S.S. Drake's range again via the Folded Data Glutton. They locate Twilight River using their ship's expanded range, then head off to this newly discovered area to pursue a signal they received. They find Winged Pikmin, and pick up a message from Louie asking for help. They manage to rescue Louie, who was captured by the Scornet Maestro, only to have him land the S.S. Drake in the Garden of Hope and steal all their juice and Charlie's rubber ducky the very next day. The trio chases the thief, and along the way, find Blue Pikmin through a path that Louie managed to open with unknown explosives. Meanwhile, Louie starts recording a log but is attacked by the Quaggled Mireclops. The trio eventually discover and defeat the Quaggled Mireclops, and take Louie back with them, now tying him up. Louie reveals the location of Olimar, and the explorers set out to rescue him at the Formidable Oak. The final fight happens against the Plasm Wraith, and afterwards, Olimar returns the cosmic-drive key, and the whole cast leaves the planet.
After arriving back on Hocotate, Olimar and Louie are ordered by the President to immediately return to PNF-404 to recover the Hocotate ship. They land on PNF-404 via the Escape Pod, making a rough landing in the Tropical Wilds. The two spend the day producing Pikmin for the rest of their time on the planet. The next day, Olimar is homing in on a signal and assumes it is one of the ship parts. Unfortunately, Olimar miscalculated and landed some distance from the Onion. After sweeping through the area in an attempt to locate the origin of the signal, Olimar and Louie can't find the ship part they came for. During the third day they explore the Garden of Hope, and locate part of the Hocotate ship. After clearing an area back to base, Olimar and Louie recover the part. On the fourth day they find and recover the Main Engine in the Distant Tundra.
The next day, Olimar and Louie attempt to track down a signal from another ship part and recover treasure from inside a cave. The two somehow get separated, but reunite before the end of the day. On the sixth day they collect treasure in Twilight River, but at the end of the day Louie eats half the fruit they found. Olimar then asked and harshly ridiculed Louie on his accessive appetite, resulting in Louie running away. The next day, Olimar searches for Louie and, after reuniting, Louie apologizes for what he did. On the eighth day, Olimar and Louie go on another expedition to collect treasure. Olimar picks up a faint signal presumably coming from one of the Hocotate ship's parts. However, after exploring, it turned out to be a signal from a fruit, which was produced by the Fruit Finder. On the ninth day, they follow signals into a cave below ground, and discover and collect the Chronos Reactor in the Formidable Oak. On the final day, the radar picks up signals from the remaining ship parts. Olimar finds a point where all the signals from parts converge, and learns that the cluster of ship parts were eaten by indigenous life-forms. Olimar and Louie retrieve the last few parts, the Nova Blaster, Repair-type Bolt, and Analog Computer, and finally repair the Hocotate ship. They finally leave PNF-404 via the Hocotate ship and head home to Hocotate.
Some undetermined amount of time after this, Captain Olimar is flying through space on his new ship, the S.S. Dolphin II, and comes across a field of asteroids. He tries to dodge them, but fails and crash-lands on an unknown planet where he discovers that the Pikmin and other creatures from PNF-404 live on this planet too. To get his ship back in working condition, he has to recover some treasures found throughout the land, so that the S.S. Dolphin II can extract their Sparklium to fuel the rocket. While exploring the planet, he rediscovers Red Pikmin, Yellow Pikmin, Blue Pikmin, Rock Pikmin, and Winged Pikmin. At some point, Olimar realizes that the ship lost an important ship part, the Sparklium Converter. Through some effort, him and the ship figure out that the piece lies in The Final Stretch. There, he comes face to face with the Berserk Leech Hydroe, and using the help of some Red Pikmin, manages to defeat the creature, expose the parasitic Leech Hydroe, and recover the missing part. With the S.S. Dolphin II refueled and the Sparklium Converter recovered, Olimar gives the Pikmin one final goodbye, and heads home safely.