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.

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.

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.

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.

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.

After getting too emotionally involved in a ninja movie, Kagura accidentally breaks Hikari's kendama toy, and thinks that he won't forgive her. However, the Ressha stops at a new Dark Station where Hanko Shadow has made everyone lose their motivation, and Right, Tokatti, and Mio fall under his spell.

After Tokatti meets a young man named Hiroki Fujisawa who seems to be unable to see the Ressha, Type Shadow sentences Tokatti to die at sunset.

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.

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.

Right managed to find one of the missing Support Ressha while out in the woods, so he and Tokatti go out to find it. However, General Schwarz has been spying on the ToQgers and heads out to capture the Support Ressha for the Shadow Line.

While the Ressha are under maintenance from the previous battle, the group uses the Support Ressha. At the next stop, Right wants to try a new buffet, but Mio meets someone apparently from her past who was in love with her.

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.

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.

After it is revealed that Mio has the weakest Imagination of the group, they try to teach her how to improve her Imagination. However, the appearance of Hammer Shadow and the strange creature Mikey complicate plans.

Soap Shadow's ability to switch people's minds and bodies switches Gritta and Mio just as Gritta is to be married to Emperor Z.

While stopping at the next station, Right, Tokatti, Mio, and Kagura are all arrested for a crime they did not commit, because the cop who arrested them is incompetent. Hikari must now try to discover the true culprit and free his friends.

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.

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 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.

Jack-in-the-Box Shadow's ability to send people flying away from him if they laugh affects all the ToQgers except Akira, leading the others to help Akira find his sense of humor or else he may be killed.

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.

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

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

In the next Shadow Town, the ToQgers come across various fictional characters, with Tokatti's favorite childhood superhero Ryo Knight appearing before him to encourage him, but all is not as it seems.