Normally in Hey! Pikmin, exploration of each area starts at one point and ends at another, and when an area is finished, the area whose letter comes next in the alphabet becomes available. But some areas have a secret exit, usually behind a hidden path or challenge. If the player finds the S.S. Dolphin II's pod at the secret exit, it will comment on how it found an extra area with some Sparklium, and will recommend Captain Olimar to go check it out. At the area selection menu, the path that opens connects to an "X" area, instead of the next letter of the alphabet. When this alternative area is completed, it leads to the letter after the area that the player skipped, meaning that regardless of the player taking the regular path or the secret exit, they will have to complete the same number of areas to reach the sector's boss area. The following is a list of areas with secret exits, and where they lead to.
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|Area||Standard exit||Secret exit||Exit location|
|1-B: Cavern of Confusion||1-C: Mushroom Valley||1-X: Cherrystone Pass||Near the end of the area, there is a patch of ground that goes down when Olimar steps on it. When it stops, there is a small fake wall to the left, leading to a doorway. On the other side, there is a wooden stake that needs 16 Pikmin to be pushed into the ground. Behind it stands the ship's pod.|
|2-C: Glowing Bloom Pond||2-D: The Shallow End||2-X: Treacherous Currents||Right before the normal exit, there is a bridge, and after that, three Bloominous Stemples. The player can fall down the bridge if it's unbuilt, or just go down through the Bloominous Stemples, and it will take them to a doorway leading to the secret exit.|
|3-A: Crystal Tunnels||3-B: Echo Cavern||3-X: The Hollow Sky||At the end of the last pit of the area, filled with crystals, there are two exits: one going to the normal exit to the right, and one to the left, blocked by a crystal. The player can break this crystal if they have at least one Rock Pikmin. On this path, the player will encounter a Crumbug, with the ship's pod nearby.|
|4-C: Pollution Pool||4-D: Space of Silence||4-X: Drenchnozzle Den||The player has to dive in one of the first ponds of the area, next to a doorway, with Blue Pikmin only. The player has to throw a Pikmin at a Starnacle's eye, in order to get access to a doorway. On the other side, Olimar has to break dirt blocks to continue in the secret path. He can go through a doorway to retrieve his non-aquatic Pikmin, before heading to the right and reach the secret exit.|
|5-B: Valley of the Breeze||5-C: Downpour Thicket||5-X: Gale-Force Glen||In the last pit of the area, there is a small branch at the left that serves as a landing spot for Olimar. After that, there's a small path that leads directly to the secret exit.|
|6-A: Scorched Earth||6-B: Lights in the Darkness||6-X: Sizzling Precipice||Near the end of the area, the player must extinguish a huge patch of fire and destroy a dirt block. However, the player must be quick, because a Fiery Dwarf Bulblax stands above the patch of fire, and will eventually fall on the player. If this happens, then Olimar must kill the enemy. Behind the dirt block stands a small path that leads directly to the secret exit.|
|7-B: Below the Ice||7-C: Over Wintry Mountains||7-X: Ordeal of Flame|
|8-C: Peculiar Rockfall||8-D: Olimar's Madcap Ride||8-X: Burning Bog|