The game opens with Diddy Kong standing on the deck of a pirate ship. In the ship's cabin, he finds a note stating that Donkey Kong has been kidnapped by Kaptain K. Rool, a pirate Kremling, who had demanded the entire Banana Hoard that he stole in the previous game for a ransom from the Kongs. Diddy Kong subsequently attempts to rescue Donkey Kong from the Kaptain, and accompanying him is his girlfriend, Dixie Kong. Together, they travel through Crocodile Isle and are helped on their way by an assortment of animals (called Animal Buddies) in a bid to defeat K. Rool and rescue Donkey Kong.
Donkey Kong Country 2 starts where the first game's final boss was located. The original game's island can be seen in the background, and the ship that Diddy Kong is on has run ashore. The first world, Gangplank Galleon, involves leaving the ship and moving to Crocodile Isle, where the rest of the game takes place.
In order to progress through the game, players must pass each stage and beat an assortment of bosses, with either or both the characters. Each stage is made up of several levels, which gets more difficult as the player succeeds completing them. There are over forty different levels which make up the several stages. In the final level of each stage, Diddy and Dixie battle a boss. The stages hold a particular theme. In, for example, the Lost World a jungle theme is omnipresent. The bosses of each of the stages relate to the stage's theme design. The player can only move onto the next world if the bosses are defeated, with the player battling K. Rool at the very end, and additionally in the unlockable Lost World.