Mother Brain has been laying siege to the Palace of Power for seven years. When it seems like all is lost, the Ancient Prophecy declares a young warrior (Captain N: The Game Master), who would lead them to victory. The Ultimate Warp Zone opens in the room of Kevin Keene, who is playing video games when he's supposed to be cleaning his room. The warp zone pulls Kevin in through his TV and his dog, Duke, jumps in after him. Kevin arrives in Video Land, at the feet of several Nintendo game heroes (Mega Man, Kid Icarus and Simon Belmont). Princess Lana tries to give Kevin his mission, but he would prefer to leave. Meanwhile, Mother Brain sends two of her incompetent goons, Eggplant Wizard and King Hippo, to kidnap Lana. After failing to stop them, Kevin tries to get the N-Team to come up with a plan. Can they save Lana in time and stop Mother Brain's forces.

Dr. Wily creates an android of Mike Vincent, a bully that used to beat Kevin up on Earth, programmed from Kevin's memories. Kevin and the android become friends, and ""Mike"" is destroyed saving Kevin's life.

Mother Brain and her minions challenge the N Team to an athletic event. Whoever wins gets the Throne to Videoland. But Mother Brain's real intention is to steal the Three Sacred Treasures from Mount Icarus. She uses them to send the N Team into the Warp Zone to Oblivion.

The N Team travels through a Warp Zone and ends up a week in the future. Mother Brain has already begun to conquer most of Videoland. The N Team goes to Dr. Wily's base to destroy the Three Sacred Treasures.

Kid Icarus is upset because he's too short. When Duke finds a magic lamp with a genie inside, Kid Icarus wishes himself big. He grows into a giant!!! When King Hippo and Eggplant Wizard steal the lamp, they make Mother Brain their servant! The N-Team, sans Kid Icarus, goes to Metroid to retrieve the lamp. When Kid Icarus comes to their rescue, he's shrunken. He uses his extremely small size to get into the lamp and wish everything back to normal. He then sets the genie free from the lamp, and the two of them become very good friends.

Dragon Lord, with the help of Mother Brain, tries to turn all the dragons on Dragon's Den evil. The N Team arrives and rescues Puff, the last good baby dragon. Using magic lightning, the spell on the dragons is removed, and Dragon's Den is saved.

Lana invites Mother Brain over to sign a peace treaty. Kevin and Mega Man are pretty eager about this, but Kid Icarus isn't taking any chances. Simon gets ahold of Kid Icarus's love-at-first-sight arrow and decides to use it on Lana. But when Mother Brain arrives, Simon mis-aims, and it winds up hitting him. He takes a look at Mother Brain and falls in love with her. Mother Brain, confused, attacks and her team imprisons Simon. This love spell will be permanent unless they shoot Simon with an antidote soon. Therefore, Kid Icarus and Mega Man have to go to Mt. Icarus to get it. So while they're doing that, Kevin and Lana head for CastleVania to find Simon. Meanwhile, over at Metroid, Dr. Wily suggests that Mother Brain have Simon prove his love to her by helping her capture CastleVania. Kevin and Lana arrive at CastleVania just in time to see that it's being attacked, and have an encounter with, making his Captain N debut, Count Dracula! Simon appears and whips Drac good, but then drops

In her secret lair within the frightful world of Metroid, Mother Brain asks a question to her all-knowing Computer Mind Mirror...who's the most fairest of them all? The Computer Mind Mirror says that Princess Lana is the most beautiful of them all and she has Eggplant Wizard to make a poison apple that'll make Princess Lana fall asleep. When this works, Princess Lana is warped to Excalibur, the land of Wizards and Warriors. Kevin, Simon, and Duke head there to rescue her. They're told that they can rescue Lana if they fall asleep, so they each take a bite of the apple. Meanwhile, back at the palace, Kid Icarus and Mega Man are also given apples and are warped to Excalibur. In their dreams, which are actually their nightmares come true, Kevin suggests that they fall asleep to wake up in their own world. It works. The N Team goes back to the Palace and they put Mother Brain and her servents to sleep.

Simon loses his memory while ironboarding. The N-Team tries to help him get his memory back. Mother Brain, meanwhile, gets King Hippo and Eggplant Wizard to brainwash him into thinking he's an N-Team hunter, Then he think he's Donkey Kong Jr. when he loses his memory again when Donkey Kong finds him. Finally, after being hit on the head with a coconut, Simon regains his memory.

Kevin, Lana, Simon, and Duke go to the Mirror World to rescue Lana's father, King Charles. Meanwhile, their opposites travel to their world. Finally, Kid Icarus and Mega Man send the opposites (except Lana's opposite) through the Mirror Warp. Kevin, Simon, Duke, and King Charles go back to their world. King Charles takes Lana's opposite back to the Mirror Warp and Lana goes back to her world safely. With the opposites and King Charles in the Mirror World, the Mirror Warp is destroyed leaving King Charles is trapped in the Mirror World.

Mother Brain tricks the N-Team into thinking she's been defeated. She then opens up a warp zone, with Kevin's neighborhood shown on the other side. Thinking it's the Ultimate Warp Zone, Kevin goes through. Mother Brain captures the remaining N-Team members and sentences them to banishment in the Black Hole Warp Zone. Kevin, who's really on Metroid, finally gets back to the Palace and rescues the N-Team.

It's Mega Man's birthday, but he's upset because he's not human. Then he finds out about the Warp of Life. He must pass the Three Challenges. He, the N Team, and Dr. Light set off, accompanied by another Dr. Light creation, Mega Girl. Mega Man passes the Three Challenges, after numerous instances of the N Team insisting that they turn back. Mega Man goes through the Warp of Life and becomes human. He then finds out that the N Team was playing along with the Warp of Life all along. They wanted to see if Mega Man really had what it takes to pass the Three Challenges. Mega Man also finds out that Roll already passed the Three Challenges, and she's alive also. Before they leave, the Warp of Life wishes Mega Man a Happy Birthday!