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.

After using all his energy while opening the tunnel to the Mountain Area, Kay collapses as he barely makes it there. Alf finds Kay in need of assistance but doesn’t step up to help him. Following Kay into the tunnel, Selly and Duck finally reunite with Alf. While Duck brings injured Kay back to Kay’s base, Selly learns that Alf was able to survive because his friends had made sacrifices.

When the avalanche starts to fall, Alf, Jeffrey, Selly and Duck quickly search for ways to protect the Mountain Area. Kay regains consciousness and helps Alf trying to stop the falling rocks, while the others build barriers. Alf still resents Kay for putting his friends in danger, and the two keep on arguing on duty. After watching Kay eagerly trying to save the Mountain Area,

Through various experiences, Kay successfully continues to receive upgrades. Feeling good and confident, he goes to the Fountain Plaza and finds out that everyone is praising Alf for being so helpful. While Alf is busy fixing things, Kay also wants to help others but keeps on causing problems instead. Kay becomes discouraged as Alf proves to be a better leader than he is.

Kay decides to train harder after finding out that he needs more experience points to earn higher level upgrades and starts working on his traction technique. While helping Kay train, Selly notices that Janne likes Kay and that she wants to help him. Selly assigns Kay’s training to Janne while she goes to install a weather station with Alf.

Kay loses control over his units because his units received upgrades after special training. He needs extra training to tame them and quickly upgrade his main system. Selly develops a simulator that synchronizes with Kay’s base system to train him in virtual space. Not knowing Selly’s hard work, Kay fights back and finally manages to take control over his disobedient units in his dreams.

Kay finds out that Alf has been training hard in the early mornings. He follows Alf to the Mountain Area and sees him running too fast on the rugged mountain railroads. When Kay asks him for the reason, Alf speaks his mind. Alf believes that he could have saved Kay and completed constructing the Intercontinental Railroad if he had gone with Kay instead of Duke.

Everyone needs more training to open the connecting tunnel to Area V so Selly installs a virtual simulation program to Kay, Alf and Duck’s main system. The three Robot Trains begin their training in their dream: Fighting against monster cakes, climbing up a high mountain and completing other unusual tasks. Then Duke appears in the virtual space.

Duke in the virtual space is unimaginably strong. After losing connection with Selly, Kay, Alf and Duck are completely exhausted, fighting against Duke. On the other end, Selly is puzzled that the program has gone out of control. While Alf wakes up from his dream, Kay and Duck are still trapped in the virtual space with the formidable foe.

The Train World is downgraded from Kay’s setback and the Area V, which requires a large amount of energy to be opened, remains unlocked. Hence the trains hold the Train Race, their tradition, which allows energy to be delivered evenly throughout the Train World. In order to win the race, the participant must receive cargos from the other trains, while running a lap around the whole Train World.

Kay and Alf tie with eleven cargos each, which they have received from helping other trains. With Kay’s Base as the last section of the race, Kay and Alf fight for each other’s cargos but end up giving all their cargos to Duck who was strolling at the bottom of the hill when the law of inertia works in Duck’s favor.