The ToQgers have managed to free Subarugahama and Tokatti has figured out a way for them to become children again, but Right is not sure what to do after transforming into Dark ToQ 1gou in his fight with Emperor Z.

Akira stops Right from taking on Emperor Z as Dark ToQ 1gou on his own as he fears for his safety and promises to fight by Right's side. Elsewhere, the other ToQgers, as children once more, go to their secret base and find something completely unexpected.

The ToQgers travel to the Hyper Ressha Terminal to meet the Rainbow Line President, and Emperor of Darkness Z decides to take the opportunity to take over the terminal himself.

The massive monster’s darkness has engulfed Right, the other ToQgers on the Resshas and the whole city. Right cannot face Zed even using the darkness and he is unable to imagine himself being victorious. Just when he has run out of options, the other ToQgers appear to save him. Then, among the darkness they can see the lights of the lamps for the Star Festival.

After the President of the Rainbow Line disbands the ToQgers, Right feels he is wrong and insists that he and the others continue the fight against the Shadow Line.

With the Hyper Ressha Terminal occupied by the Shadow Line forces, the President decides to authorize the ToQgers to use all thirteen of their Ressha together to get it back, but first, they must get the Drill Ressha back from General Schwarz.

With Christmas approaching, Imagination begins to run wild which makes the Shadow Line weaker. Right, however, realizes Akira is missing, while General Schwarz plans an offensive against Emperor Z and various defeated Shadow Creeps suddenly revive one after another.

The ToQgers arrive at a train station taken over by the Shadow Line which has been renamed "Kettougahara", controlled by the Shadow Line's Saber Shadow who makes everyone duel. The ToQgers do their hardest to protect a boy who is scared at what the Shadow Line has done to his neighborhood and figure out a way to end the Shadow Line's control.

The Conductor reveals that he has commissioned the transformation items for the sixth ToQger, and a Rainbow Line maintenance worker named Zaram, a former member of the Shadow Line, has not been chosen to be ToQ 6gou.

The ToQgers must defeat Miss Gritta and General Schwarz while trying to recover their memories of their long lost home town.

After Ticket warns the ToQgers that the Ressha trains will not wait for them, Kagura is left behind and despite her fears must take on Chain Shadow by herself.

Although Zaram has left the Shadow Line and has become ToQ 6gou, he does not wish to remain with the ToQgers. When Ring Shadow traps people by putting rings with their names on their heads, Zaram, who should have eschewed his old Shadow name, must find a way to help the ToQgers and escape his former shackles as a Shadow.

While the ToQgers enjoy a day out at an amusement park, Right meets a young man with balloons who seems odd. Baron Nero leads an offensive against them in order to welcome the Emperor of Darkness onto the Shadow Line, and also has a particular interest in the man with the balloons.

While Tokatti is trying to befriend Akira, the Ressha gets trapped in a mine collapse orchestrated by a Kurainer Robo, forcing Tokatti and Akira to work together to find ToQ 6gou's personal Ressha.

The Rainbow Line makes an abrupt stop at a river, requiring the use of the Car Carrier Ressha to cross, but their Imagination is not enough to power it. As the other ToQgers try to come up with a way to cross, Bucket Shadow starts to collect darkness by making people feel hungry via eating every scrap of food from them.

Tokatti and Kagura uncover a Shadow Line plot to make children unusually happy, but Kagura must also deal with the young girl Aoi who says her brother has been kidnapped by the Kuliners taking children throughout the city.

Mio suddenly recovers a memory of their hometown, in that around this time of year they had a festival for the stars, and Right remembers as well. As they search for their hometown, the wedding of Emperor Z and Miss Gritta commences, and General Schwarz takes over the Ressha in the ToQgers' absence.

To find their hometown Subarugahama, the ToQgers must move the Ressha onto the Shadow Line to free it from the darkness engulfing it, but the shadows engulfing the junction point keeps them from using their powers

Right tries to use the Hyper Ressha to liberate the next Shadow Town, but his body cannot handle the strain. Elsewhere, new members of the Shadow Line appear.

With their memories back, Right and Hikari must use their training in karate from Right's grandfather to defeat a Shadow Monster who has turned the people around the next Dark Station into his fighters, rather than Kuros.

When having some time off at a station stop, Tokatti loses his Rainbow Pass somewhere, forcing him to follow the others on standard forms of transportation. While Right, Hikari, and Kagura battle Stove Shadow, Mio helps Tokatti search for his missing pass.

When the evil Shadow Line begins to use their evil train the Kleiner to kidnap children, a young man named Right is amongst those nearly captured. He then sees the prismatic Rainbow Line and its Ressha trains appear, along with four of the ToQgers, inspiring him to help protect the children with them.

The other ToQgers can no longer see the Ressha and are seemingly devoid of their Imagination. Right tries to get through to them, but Lamp Shadow reveals to him that Z has hypnotized all of them to forget their time on the Rainbow Line. Right must figure out how to get them back to normal, while also dealing with new memories of their childhood home.

The signal from the lost Diesel Ressha is found, but because it is so weak there might be a chance it cannot work again. Right is sent out to find it, as his strong Imagination can restore it. They learned that the previous enemy they encountered placed a bomb on Tokatti that is strong enough to destroy the Resshas, when the Ressha's brakes are discovered to be broken, everyone fears that the Shadow Line has planted a bomb on them.

A series of attacks from Kuliner Robos leaves the main Ressha in dire need of repairs, once again leaving the Support Ressha and Diesel-Oh all that the ToQgers can use. The Conductor warns them that they must find other Support Ressha in order to bolster the powers of Cho ToQ-Oh. While Right and Mio are out searching, Loupe Shadow appears, and throws Mio into a powerful rage.