Pikmin: Clouded Skies

Plot
In Pikmin: Clouded Skies, you play as Captain Olimar and his faithful assistant Louie. The goal is to collect treasure and discover all monster types and destroy Jaaku's company.

This takes place about a year after the second game. The President of Hocotate freight decides he would get more money if he researched the planet and its inhabitants rather than if it was a delivery service. Thus, the Hocotate Planetary Research Company (or HPRC) was born.

Olimar and Louie soon set out to the Pikmin Planet yet again, unknowingly, some employees of an old company rival, Jaaku's Package Delivery, follows them to the planet. After some spying, spelunking, and general exploring they return to Planet Hocotate and relay information to their boss, Jaaku, telling him everything. They soon set out and secretly travel to the Planet of the Pikmin. After exploring an underground cave, they discover a metal that is a large energy source on Hocotate, the only difference is this metal's power is triple the the power of the metal on Hocotate. It is also good because on Hocotate, this metal is becoming very scarce. They start mining it and selling it on Hocotate and the become a very successful mining company.

Meanwhile, Olimar is searching for the Pikmin and researching the animals on the planet. Soon he stumbles upon one of Jaaku's mining squads, while they were mining this new wonder metal. He goes back to his camp and relays this information to the President and he decides to confront Jaaku. Jaaku says that it isn't any of their business what he is doing on the planet and that the President should "keep his nose out of other people's business". After a little spying, Olimar discovers that the mining is hurting the environment, and the creatures that live on it.

Soon Jaaku's mining company has amassed more money than he thought possible. They start to expand their mining empire and spread to other lands and caves. It soon stretches from desert wastelands to snowy hills. The planet is abundant with this wonderful element. Soon Jaaku's greed becomes so great, that he decides to do something with all of the planet's flora and fauna. He decides to kill some of the animals and use their parts to make more products, but, they find that they are loosing too many men and are loosing money on his project. So after spying on Olimar they attempt to befriend the Pikmin but to no avail. Then they end up capturing a few different types of Pikmin and experiment on them. They soon make a sort of robotic Pikmin that is resistant to the harsh elements, save electricity, explosions, and water. With these robotic Pikmin, they end up capturing the creatures and mind controlling them for their own insidious purposes, as well as killing them to make products and food to sell.

Soon Olimar decides they should strike back. Olimar gathers up his Pikmin squad and slowly starts destroying the various camps while also collecting treasures on the planet to sell. He soon reaches the Citadel, where the evil, Jaaku is residing, watching the planet's ecosystem crumble beneath him. With the help of his old, and a few new Pikmin friends, he destroys the Citadel and reaches Jaaku's underground Lair. Jaaku unleashes his ultimate experiment: a giant mutated Emperor Bulblax. This version of the Emperor Bulblax has a spiky tongue, abnormally large eyes, bigger, stronger, and immune to bomb-rocks. After its defeat Olimar captured Jaaku and put him in jail and slowly nursed the planet back to health, and finished his research expedition.

Areas
Listed in order discovered:
 * Ivy Forest
 * Ancient Temple
 * Dank Abyss
 * Dusty Desert
 * Ruined Earth
 * Hollow Fields
 * Citadel
 * Beauty Beach

Grub-dog family

 * Red Bulborb
 * Purple Bulborb
 * Dwarf Red Bulborb
 * Albino Bulborb
 * Dwarf Albino Bulborb
 * Yellow Bulborb
 * Bloated Bulborb
 * Freshwater Bulborb
 * Scaly Bulblax
 * Saltwater Bulborb

Dirigibug family

 * Careening Dirigibug
 * Icy Dirigibug
 * Dirigible Stickybug

Wriggler family

 * Centipede
 * Squeekapillar
 * Wriggler

Dweevil family

 * Black Dweevil

Shark family

 * Chomper

Jaaku's minions

 * Bulborb Rider
 * Hunter
 * Miner

Amphituber family

 * Subterranean Wogpole
 * Yellow Wollywog
 * Wollywog
 * Wogpole
 * Willywog
 * Crogpole
 * Croggywog

Skitterling family

 * Skitter Leaf
 * Mimirock

Bosses

 * Incinerator Mech
 * Maestro Miner 9000
 * Titan Wriggler
 * Puffstool
 * Burrowing Snagret
 * Pileated Snagret
 * Emperor Bulblax

Pikmin

 * Red Pikmin
 * Yellow Pikmin
 * Blue Pikmin
 * White Pikmin
 * Purple Pikmin
 * Bulbmin
 * Grey Pikmin
 * Black Pikmin
 * Mushroom Pikmin

Weapons/sprays

 * Bomb-rock
 * Bug Spray
 * Icy Bombrock
 * Sticky Bombrock
 * Ultra-bitter spray
 * Ultra-spicy spray