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.

It's the day of the opening ceremony for Kay to finally open the tunnel to Area V. Everyone is in the festive mood, but Kay seems nervous because he will be put to the test as to check how much he has improved. Sensing something strange on the night of the Train Race, Jeffrey is gone to check on Duke in his jail. As everyone cheers Kay on, Duke shows up at the ceremony.

Kay and his friends battle against Duke. Even after Alf ties Duke up, Duck shoots his water guns at him and Selly uses the G-force Nanobombs to help Kay fight Duke, all their efforts are useless against the powerful enemy. But when Kay and his friends refuse to give up, Duke starts up his engine to suck in all the energy from the Fountain Plaza and causes a blackout.

To make matters worse after all his friends have fallen, Kay's vision sensor is broken. Jeffrey tries to fight off Duke but he's no match for Duke. Not being able to see, furious Kay lunges at Duke, but Duke sends a shock to Kay's engine, making him immobile. Alf, Selly and Duck come to Kay's rescue, combining their skills and weapons to protect Kay.

As the tunnel to Area V reopens, Victor is back. Victor visits the gatekeepers of each area who are his old students. Watching everyone welcoming Victor, Kay realizes that Victor is very much respected around the Train World and feels sad that he doesn't have any memory of Victor. After meeting everyone, Victor takes Kay to meet Stella, the fortune teller.

Kay listens to Stella's story about the primordial train called the Alpha Train. Stella warns Kay that soon, darkness will dawn upon them. Kay is doubtful but Victor shows him the proof of the Alpha Train's existence, the cargo of the Alpha Train that has landed in Area V. Victor explains to Kay that Area V was able to survive after it was shut off from the Fountain Plaza.

Kay and his friends realize that Duke has acted strangely because of a virus. To treat Duke, Kay and the gang must log into Duke's system and remove the mutant virus themselves. With the help of Selly, Kay, Alf, Duck and Victor enter Duke's system.

While Kay and his friends are searching for the virus inside Duke's memories, they find Duke's memory of the day before the opening ceremony of the Intercontinental Railroad, where a virus infected Duke's system and turned him evil. They now know that Duke was a victim of the virus. Fighting the mutant virus monsters, Kay and the friends get closer to the central part of Duke's engine.

Duke finally comes back to the Fountain Plaza after his recovery, but everyone is still scared of him. Kay asks Duke to go training with him, but it is actually Kay's scheme to help Duke earn trust back from the other trains. Up on the mountain, Kay and Duke pick up things that the others might like, but the other trains still can't believe Duke's good intentions.

Kay loses control of his engine and starts to run too fast, causing space-time to warp and twist. Kay visits the Fountain Plaza and notices that everyone is moving very slowly. Duke is the only one who realized what's happening to Kay and comes to help. When Duke tells Kay that no one can see or hear him because he's moving too fast, the Time Tunnel opens up.

Kay arrives at the Central, but the atmosphere is somewhat different than before. His friends act weird and seem to be afraid of him. Kay hears from Duck of what he had least expected. In this world, Kay is a betrayer who interrupted the opening of the tunnels and shut down Duke's engine. In a nutshell, it becomes clear that Kay had arrived in a whole different Train World.

Due to the prolonged isolation period, Area V's energy level is unstable, and the snow starts melting, causing the Ice Cave to collapse on Victor while he is investigating the cave. Kay and Stella save Victor, but Victor needs Selly's help immediately. But because of a rise in the temperature, the entire Area V is melting, hindering Alf, Duck, Selly and Duke to get to Victor.

Everyone safely makes it to Victor's Base. There, Selly connects Victor's engine with Kay's while repairing Victor. Meanwhile, Duck is skating on a frozen lake when suddenly, the ice on the lake melts and all the water evaporates! Alf and Duke discover what has caused the situation and head out to find the source.

One morning, a train is found thrown off the track, all out energy. While everyone watches him worriedly, the train wakes up, pointing the finger at Duke as the attacker. Everyone starts to suspect Duke again and asks him for an explanation. Kay fights for Duke's innocence, but Alf and Duck also start to get suspicious of Duke. At last, Duke declares that he'll get locked up.

Duke's duplicates show up in the Fountain Plaza. It turns out the virus has duplicated Duke while it was invading Duke's system. Victor, Alf, Duck and Selly fight against the duplicates, and Kay and Jeffrey join their effort when they get back. Meanwhile, Duke, locked-up in the cell, senses that something has gone wrong.

While fighting Duke's duplicates, Kay and his friends realize something odd. Even though the engines of the Duke's duplicates have ceased to operate, they are still moving. It turns out Duke's duplicates are using the energy from the Fountain Plaza to activate themselves, and because of that, other trains cannot recharge properly.

All the trains evacuate to Area V, and the Robot Trains block the tunnel that connects to the Fountain Plaza. But Duke's duplicates penetrate and come through the tunnel, endangering everyone in Area V. Then Duke arrives to Area V just in time. It turns out Becky has unlocked Duke while everyone evacuated. Only thing that can stop Duke's duplicates is the energy coming from the Alpha Train.