Yuuta Kobayashi spends a long time playing Mega Man 5. When he falls asleep without shutting his console off, Dr. Wily decides to leave the game enter the real world. The next morning, Mega Man and Rush follow Dr. Wily into the real world, much to the surprise of Yuuta, his older sister Akane, and their parents. Yuuta's father volunteers to take Mega Man to Tokyo, where they expect Dr. Wily to be headed. Mega Man and Rush follow Wily's trail to an amusement park. As Mega Man begins to attack, Wily rallies all his robots to attack!

Yuuta is preoccupied with his Mega Man game on Omisoka, and isn't going downstairs to celebrate the holiday with Akane and his parents. He and Akane hit the console by accident after arguing. This means Mega Man is again transported into the real world, so he gets to celebrate New Years' Eve with the Kobayashi family. After learning about otoshidama and watching the celebrations on TV, Mega Man finds out that Dr. Wily ended up at Dr. Light's lab, stole Dr. Light's newest creation, a time machine, and kidnapped Roll.

Mega Man and Roll get pulled out of the game world by Yuuta and Akane and are taken to the Obon matsuri. Mega Man and Yuuta carry the mikoshi in a parade, Roll learns about yukatas and makes a promise with Akane that she will wear a kimono on Shichi-Go-San, Mega Man learns about cotton candy, Roll plays Whac-A-Mole, and the kids watch the fireworks. During the time everyone is gone, Dr. Wily escapes the game world with his updated Skulker and kidnaps Proto Man.