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While Olimar is away on his vacation, The company he works for, Hocotate Freight, falls into serious debt due to a terrible accident in which an entire load of golden Pik-Pik carrots is eaten by a ravanous space bunny. The President of Hocotate Freight recruits Captain Olimar
and the new employee, Louie
, to return to the planet of the Pikmin to collect funds. The President sends letters to the two and tells of his hard life back home, which includes living homelessly under a bridge, amoung other things.
When the debt is finally settled, Olimar returns home only to find that Louie was left behind, and him and the President return to find him. During this time, the President replaces Louie as the second playable character. In the end, it is found that Louie ate the golden Pik-Pik carrots, causing the entire crisis from the get-go. He is also a trophy that you can get in Super Smash Bros. Brawl.