What happens to Louie in Pikmin 3?

Louie is lost twice over the course of the game.

The first time, in the Valley of Repose, you have to aid the Pikmin with Olimar to reestablish communications with Louie. By pressing "Y" after the ship has established communications with Louie, you will be able to control him. He is originally located on the opposite side of the land. Simply walk him over towards Olimar if you wish to reunite them.

The second time, after you pay off Hocotate Freight's debt, Louie can be found at the bottom of the Dream Den, a very challenging cavern located at the far side of the Wistful Wild. It is best to bring every color of Pikmin into this cave. The "final boss," as you can complete the caves in any order, is located in the Dream Den. Louie is being controlled by a large spider, and will be saved after you defeat it.