Windmill Hills starts out in a small glade containing several Cheesy Chesters and Hootzes, as well as a row of spinning windmills with spinning platforms. The player must use Dixie Kong's flying ability to get over the gaps and jump on larger enemies such as Pufftons, after which there is a Checkpoint. Following a Schnautzel, DK and Dixie will navigate more windmills, this time which spin faster than the ones before the checkpoint.
After landing on a small patch of land where a Cheesy Chester randomly comes out, the Kongs will go through a series of Barrel Cannons, which take them across more windmills, between which are several Bananas, after which there is a similar windmill where they will receive Red Balloons if all the Bananas are collected. Soon after this, there is a Burlap Hanging Sack containing one of the level's Puzzle Pieces that must be opened by throwing the Diddy Kong barrel at it, which will switch Dixie out with him. Diddy's jetpack ability works similarly to Dixie's hair, still allowing the Kongs to fly short distances. Following that, DK and Diddy will enter a windmill and go up a stack of spinning gears, which have platforms that rotate rhythmically. There are also Pointy Tucks on the platforms, which cannot be jumped on. Upon getting to the top, the Kongs will go on a large platform attached to a long cord (acting as a slow zipline) which leads them to another area with a windmill containing bells that have to be rung (which ends up giving a Puzzle Piece), as well as the letter "N". Following this, DK and Diddy will go through another series of Barrel Cannons, this time flying through a wide area with fall-colored trees and more windmills with items, after which they land on a platform containing the Slot Machine Barrel that ends the level.
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