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After being defeated by the Battletoads, the evil Dark Queen flees to the outer reaches of the universe and the 'Toads and their mentor get on with their lives. However, one day the Earth's military is neutralized and a giant spaceship called Colossus emerges from the moon. Apparently, the Dark Queen is back with another plan to dominate the galaxy, and she has allied herself with the Shadow Warriors (from the Double Dragon series) to supplement her forces. Deciding to even the odds, the Battletoads get in contact with Billy and Jimmy Lee and ask them for their help. The brothers agree, and all five immediately take off for the Colossus in a mission to stop this two-pronged threat.

The player has a choice of five playable characters: Billy and Jimmy Lee from Double Dragon, and Zitz, Pimple and Rash from Battletoads. The player must then proceed through seven stages, kicking and punching each enemy that comes onscreen. A boss is included at the end of each stage, challenging the player before they can progress to a higher level of the game.

With two players, the continues are overlapping: whenever one player continues, then both players have to start at the beginning of the level, where a strong player can tow a weak player along to advanced levels; in Battletoads Double Dragon, a weak player will hold a strong player back).