King Hippo and Eggplant Wizard have given a deadly computer virus to the Palace of Power, and accidently infect Mother Brain putting her into a coma. Asking the N-Team's help to save Mother Brain, Captain N, Princess Lana, Kid Icarus, and Duke shrink themeselves and enter Mother Brain's mind to search for a virus antidote. They run into evil duplicates of themselves being fought by a young girl. She tells them where to find the antidote while fending of the duplicates. The N-Team escapes and save Mother Brain and the Palace of Power, revealing that there is good inside of everyone.