The Final Trial
First you must start by making your way down to the final boss. Start by taking about 30 blue Pikmin over to the first platform and get them started on the bridge. Next take about 10 yellow Pikmin and start throwing them across to get them up to where the bombs are located, just east of where the blue Pikmin are building the bridge.
Next grab about 30 red Pikmin and make your way across the bridge with the fire to the west side of the level. The red Pikmin are the only Pikmin who can cross this bridge. Use Olimar's whistle (B) to guide them across the bridge from down in the water, as Olimar can't actually go on the bridge himself. Then get them started on moving the box at the end. In the meantime, get the rest of your Pikmin started on the second bridge.
Lastly, destroy the wall blocking you from the boss. In this room, make sure you walk around the plant thingy in the middle. That's him, but your not done yet. Go to the other side of the room and breakdown that door. Then load up some yellow Pikmin with bombs. It may be a good idea to rearrange your team of Pikmin before you fight. I suggest 30 yellow and 70 red.
The move he does when he sees Pikmin is his little tounge whip thing. All you have to do is throw a Pikmin at him, a yellow one holding a bomb, have him swallow it, and then he will be temporarily disabled. Quickly get your other Pikmin and throw them onto the enemy until he is defeated. Remember to call them back when he gets back up. Repeat to defeat.