You must start the game from Stage 1. Bongo is a character that looks like a rabbit (a guy in a costume). As you play through the game, you will see trees that can be hit. They will give you life and once the tree is done dropping fruit, Bongo will pop out of the tree with a sign to tell you there is no more.
Stage 1 - Downtown Tree: You will see this just as you are about to pass by the Fire Station.
Stage 2 - Krustyland Tree: After defeating the tea cup enemies, you'll see this to the right (in front of the cages).
Stage 5 - Springfield Butte Tree: You'll see a tree early on in the level after seeing the ape enemy that sort of resembles Homer. It has a bees nest on it. Hit the tree and try to avoid the bees. Once they fly away (or hurt you), then hit the tree more.
Stage 7 - Channel 6 Tree: When you get to the area with the ninja enemies, you will see the pink tree. After Bongo appears, you will get the achievement. There is another tree following just in case you missed the first. Only one of them has to be hit.