Leader
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The Pikmin Leaders, often also called Captains, are the characters of whom the player has control. In the first game, there is only Olimar, an employee of Hocotate Freight who crash-landed on the Planet of the Pikmin. In Pikmin 2, Louie is added as a second character, also controlled by the player; it is possible to switch between the two playable leaders by pressing the Y / 
button. Louie is replaced by The President after the debt is cleared. In Pikmin 3 there are three new leaders: the engineer Alph, the botanist Brittany, and the crew's captain, Charlie.
The leader is followed by Pikmin they have called out of the Onion or plucked, and by lone Pikmin they touch or whistle at. The leader can throw Pikmin for various purposes, or attack monsters themselves when no Pikmin are nearby. Puffstools, Antenna Beetles and mature Bulbmin act as naturally occurring enemy leaders, in each of the two Pikmin games, stealing the player's Pikmin or scouting with their own.
The inactive leader is controlled by a simple artificial intelligence in both Pikmin 2 and Pikmin 3. If the inactive leader is with the active leader's group, he or she will follow the active leader very closely. They will also attack an enemy if the active captain is attacking the enemy through punching. However, they can only throw about one punch per second; far less than the player is capable of. The Rocket Fist will also not activate for the inactive leader.
If an inactive leader is not in the player's group, they will stand idle similar to the way Pikmin do when dismissed or thrown. However, they can not call idle Pikmin to their side by touching them. They will also not attack enemies; instead choosing to walk away from them, which can be used to the player's advantage against certain creatures, such as the Ranging Bloyster. Pikmin in the inactive group are likely to be killed in these situations nonetheless, as the leader's reactions are rather sloppy and aim to protect the leader, not his or her Pikmin.
Olimar
- Main article: Captain Olimar.
Captain Olimar, often simply called Olimar, is the main character of the Pikmin series. He is the Hocotate Freight employee who discovered the Planet of the Pikmin. He is the captain of his personal ship, the S.S. Dolphin, until it is sold to repay some of the debt at the start of Pikmin 2. His family consists of his wife, his son and his daughter, who live on Hocotate and remain there throughout the two games in the series. Captain Olimar is only playable in Pikmin 3 in Bingo Battle and certain Mission Mode levels.
Louie
- Main article: Louie.
Louie first appears in Pikmin 2 and serves as a partner to Olimar, commanding Pikmin as his sidekick. He is relatively new to the shipping business and has a ravenous appetite. He was raised by his grandmother who made him play with bugs and eat them, from where it is assumed that his great affinity for cooking beasts in Pikmin 2 comes.
After gaining 10,000 Pokos, Louie is replaced by the President. This is because Olimar accidentally leaves him behind on the planet on his return to Hocotate and only realizes this, shown in a cut-scene, as the ship begins to speed away. The actual reason, however, is never stated. It is unlikely that he jumped out after having taken off on purpose, as he is in a rather shocked and frightened state (noticeable in the credits cutscene, though that may be due to having been left behind).
In the end, it becomes apparent that Louie is actually the one responsible for the debt Hocotate Freight suffers, and not a "ravenous space bunny" as he lead the President to believe at the start; it was truly he who ate the load of Golden Pikpik carrots. This is revealed in a cutscene unlocked by getting a pink flower for all 30 of the Challenge Mode levels.
In Pikmin 3, Louie is only a playable leader in Bingo Battle and certain Mission Mode Levels. In Mission Mode, he must first be brought back to the SPERO before he can used as a playable character.
President
- Main article: President of Hocotate Freight.
The President is the owner of Hocotate Freight, and is a playable character in Pikmin 2. He is called "Shacho" in the Japanese version, which is Japanese for 'President', and is often called by that name because he says it when the player switches to his character. After returning back to Hocotate after clearing the debt, the President becomes the replacement for Louie for the rest of Pikmin 2's duration. Template:Endspoiler
Alph
- Main article: Alph.
Alph is the mechanic of the S.S. Drake. He is very interested in technological devices and is a very capable engineer that configures objects found on the Pikmin Planet for the crew to use on their quest for food. He has a blue tuft of hair and wears a spacesuit with blue highlights. Like the other two members of his team, he is from Koppai.
Brittany
- Main article: Brittany.
Brittany is a botanist who is responsible of keeping track of the fruit found on the planet and juices produced by the crew. She is a bit dishonest and seems to care about her own safety far more than that of others, as she tends to take slightly more than her share of juice and isn't concerned at all when Charlie is lost in the wild. Brittany is also a bit of a glutton, though not quite as much as Louie. She has shoulder-length pink hair and a spacesuit with pink highlights.
Charlie
- Main article: Charlie.
Charlie is the captain of the Koppaite trio. He is brawny with dark-brown hair in a buzz-cut. Though acting tough, he is caught quite off-guard by the Pikmin on the foreign planet. He tries his best to appear as a good leader, but nonetheless the crew members all have equal say in decision-making. His suit has green highlights and also bears a five-point star, which presumably denotes his superior rank. He also has a rubber ducky that he is very fond of.
Enemy as leaders
Puffstool
- Main article: Puffstool.
The only enemy leader in the first Pikmin game is the Puffstool, who will shoot spores at Pikmin to possess them. These "Mushroom Pikmin" will follow the Puffstool around, and will chase Captain Olimar if he gets too close. Pikmin can be cured by either shaking them off or by killing the Puffstool.
Antenna Beetle
- Main article: Antenna Beetle.
The Antenna Beetles found in Pikmin 2 are comparable to the Hocotatian leaders in that they can control Pikmin with the sounds they produce, apparently by flapping their wings. This appears to affect Pikmin in a similar way to the whistles of the other leaders. The only way to regain control of the capture Pikmin is to kill, stun, or chase away the Antenna Beetle. The Antenna Beetle's whistling range is notably larger than the leaders' without the Mega Tweeter.
Bulbmin
- Main article: Bulbmin.
Bulbmin are Pikmin-Bulborb crosses that roam around caves. They have a maximum of 10 following Bulbmin. These Bulbmin do not do anything but follow their leader. The leader attacks by eating Pikmin just like normal Bulborbs do. When the player kills the Bulbmin leader, the followers will get frightened and run around in circles. These Bulbmin can be called into the army, and act as additional Pikmin. They have immunities to the main four hazards, but the downside is that they cannot be taken out of caves. It is best to use Candypop Buds to convert them into other types of Pikmin which can be taken out of caves.
Scornet Maestro
- Main article: Scornet Maestro.
The Scornet Maestro is the fourth major boss in Pikmin 3 story mode. It can command up to 100 Scornets at the same time and use them to attack with various formations. They also protect it. After one of its assaults, the Scornets will leave for a while, and the player will be able to attack the Maestro.
Leader is down
When a leader loses all of his or her health, they become unconscious. In Pikmin, the day ends and all Pikmin that aren't in an Onion die. In Pikmin 2, this only occurs if both leaders faint; otherwise, the Pikmin that were with the leader become idle, and the leader is moved to the ship, where he lies on the floor until the end of the day.
In Pikmin, if Captain Olimar's suit takes too much damage, there will be a cutscene with his space suit being electrified, then Olimar falling down. Eventually, the screen will turn black and white. The words "Olimar is down" will then appear on-screen and the day's journal will read as follows:
"I've been careless, sustaining damage beyond my space suit's limits. My crisis transport system saved me, but I lost all of the Pikmin I had with me. I must pay closer mind to my space suit damage meter in the bottom-left corner of the screen. I can press A by the Dolphin to repair my suit."
Trivia
- In Pikmin 2, when the active leader is Louie or The President, the background music is in swing time, while the music has straight eighth notes when the active leader is Olimar.