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 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.

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.

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 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.

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.

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

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.

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.

In the next Shadow Town, Keeper Knight forces the ToQgers to take a quiz, leaving Tokatti unsure of how he should answer due to being asked about Mio.

The Ressha stops at a station under the power of Film Shadow, leading the ToQgers to help produce a rival movie to defeat the monster.