After being influenced by the power of "Number 34: Terror-Byte", Mr. Kay created the virus, which was manifested on-screen similarly to his own "Crashbug" monsters. The virus infected all electronic devices around Heartland City by infiltrating the host computer. It caused various malfunctions, such as traffic lights quickly changing colors, vending machines spitting out free drinks and Litterbots perceiving citizens as trash. Kari Tsukumo was unable to complete her work due to the virus and ordered her younger brother, Yuma Tsukumo, to find out what was going on. According to Kari, If the virus continued to infect systems, terrible things could happen, like hospital and bank networks going down.
Kari discovered that the virus had been sent from Heartland Academy and sends Yuma and his friend Tori Meadows to the school's library, knowing the culprit would have to go there to access their own personal computer. They believed that Caswell was the culprit after his monitor filled up with Crashbug images, but he revealed he was trying to find the culprit as well. In the process, he accidentally launched another round of the virus, which will fully infect the city in thirty minutes. Using his own hacking skills, he found the location of the original hacker. They find Mr. Kay there, and seeing Kay possessed by a "Number", Yuma and Astral ask to Duel him. He agrees, adding that he will disable the virus if he loses. At the same time, Kari attempts to hack in and stop the bomb herself, having to go through a virtual maze to do so.
Meanwhile, Kari makes it through the maze, where she finds that she must defeat a Crashbug avatar with her own to stop the bomb. Kari defeats the on-line virus, while Yuma defeats Mr. Kay. Despite this, the virus bomb is not stopped. When it goes off, nothing appears to happen. Mr. Kay tells them to look at the sky while wearing their Duel Gazers. They see a giant, virtual "Crashbug". Kay explains that he needed to launch the virus bomb in order to turn on and off lights in certain buildings, enabling the whole city to see the "Crashbug" image. Mr. Kay had done all this in the hopes that doing so would cause what is written in the lore of "Crashbug" to be made true - "An electrical fairy that lives off of the other bugs. It becomes extremely powerful because it lives off its bug friends. It's said that those who witness its full moon-like appearance may forever live in happiness".
When Yuma and the Number Club need to find the hideout of Kite Tenjo, Caswell goes to Mr. Kay for help. He asks him to use the Crashbug Virus to pinpoint the hideout's location. Kay doesn't wish to help, but Caswell blackmails him, saying he'll tell everyone it was him that originally launched the virus if he doesn't help them. Kay complies and successfully finds the hideout, using the virus to crash the hideout's computers systems.