

While playing football, the N Team warps to Faxanadu, which is the home of two races: the Elves and the Dwarves. While trying to get back home, Kevin and Simon decide it would be more fun to see who gets back home faster, so they divide into teams. Each team is led to believe that the Elves or the Dwarves stole a powerful crystal from the other race. Only Lana has enough sense to know that the others are behaving like little kids. Then, a being known as The Evil One gets the crystal. With it, he plans to destroy Faxanadu. Only when everyone works together are they able to overcome the power of the crystal. The crystal is destroyed, and The Evil One vows to return.
King Charles is about to come home through a warp zone that only opens every 1000 video years. But he decides to send a supercomputer called Game Boy in his place. Game Boy turns out to be nothing but trouble for the N-Team. Mother Brain gets Game Boy, and Dr. Wily turns him into Game Brain. When the N Team comes to Metroid to rescue Game Boy, Game Brain sends monsters after them. Duke comes to the rescue, pulling the cords out of Game Boy with his teeth! The monsters disappear. Back at the Palace, the gang officially welcomes Game Boy to the N-Team.
The N-Team is invited to Kongoland by Prince Plenty. Dr. Wily invents a brain swapper so Mother Brain can get a body. She chooses Princess Lana as the donor. However, when they go to Kongoland, Donkey Kong kidnaps Mother Brain and Game Boy. The brain swapper is accidentally attached and activated. Donkey Kong gets Game Boy's body, Game Boy gets Mother Brain's body, and Mother Brain get Donkey Kong's body. Simon and Kevin go to find ""Gape Boy"", Kid Icarus and Mega Man search for Game Boy's ""brain-in-a-bottle"", and Lana decides to give ""Mother Kong"" a makeover. Donkey Kong's family elect Simon their new leader! Everyone's brain is swapped back to the right place, and the Kong family carries Simon off.