The Train World is having a busy period, building railroads between continents. The Intercontinental Railroad construction is to revitalize the isolated continents by installing connecting railroads. The main supervisor of the construction, Kay, begins the construction despite worries from other trains. But Duke, who is to work together with Kay, betrays him and tries to steal his magnetic engine.

Duke returns to the Train World and lies to everyone that Kay is lost due to an unfortunate accident. But Kay also makes it back, and Duke's lie is revealed! To fulfill his evil scheme, Duke forcefully tries to take over the Train World. But with his last ounce of strength, Kay stops Duke using his lethal combat technique, Maximum Overdrive.

After a long rest, Kay wakes up, clueless to who or where he is. Confused, Kay leaves his base and arrives at the Fountain Plaza. There, everyone welcomes Kay, but Kay doesn't remember anything about his friends. He goes sullen after listening to how great he used to be, and his friends decide to help him get back to his old self.

As the power of the Train World becomes weaker, viruses spring up and begin to infect the inhabitants. If infected, the trains lose control of their engines and run until they completely exhaust their energy. While Selly searches for the vaccine, Kay and Duck enter the infected zone, Area D. The virus has already spread throughout the region, putting trains in danger.

A virus enters the system in Area D, and the area's control unit malfunctions. To fix the problem, Kay has to run faster than the flow of energy and manually adjust all levers along the train tracks. Confident about his speed, Kay thinks this will be an easy task, but a gorilla speedometer surprises Kay, chasing him as it grows bigger and faster, collecting energy from the tracks.

After Kay gets his upgrade with Experience Points from completing the Area D restoration task, he decides to reopen the railroad tunnel to the Mountain Area, where Alf is trapped. With everyone cheering for him, Kay opens the tunnel gate that leads to the Mountain Area, but his attempt is hindered by a fiercely cold wind from the tunnel that freezes the Fountain Plaza completely.