A luckless boy named Ryotaro Nogami comes across a strange train pass and becomes possessed by a powerful demon as he finds himself unexpectedly becoming the a hero known as Den-O fighting strange creatures from another time.
Ryotaro discovers more about his duty as Den-O to protect the timestream as he tries to figure a way to appease Tetsuo before the Bat Imagin can ruin the past.
With Urataros causing nothing but trouble, Ryotaro is forced to make a decision regarding whether to keep the lying Imagin around while he and Hana try to figure out the Imagin's contract holder.
Momotaros tries to prevent Urataros from causing too much chaos with Ryotaro, while Ryotaro sparks the jealousy of a boyfriend of a girl he is forced with, leading to a drastic confrontation.
Both Ryotaro and his sister Airi work to try and improve relations between the broken couple as Den-O tries to figure out the mystery behind the Imagin's attacks.
Ryotaro and Hana pursue two Imagin attacking martial artists, one to eliminate rivals while another only to prove its own strength against other opponents.
Ryotaro tries to discover the truth regarding the karate champion possessed by the Rhino Imagin, while Hana tries to make sense of the Bear Imagin and what he really desires.
After discovering the Imagin contract holder is Kasumi's father, Ryotaro tries to discover why as Kintaros keeps trying to manage resolving the crisis in his own stubborn ways.
Ryutaros continues to cause problems to the other Imagin in holding on to Ryotaro's body, forcing them to take action in order to get their partner back.
As he remains hostage by the bathhouse owner, Ryotaro tries to figure out the mystery of his relations with his former boss while trying to prevent Ryutaros from dealing with him his own way.
Ryotaro and Hana decide to clamp down on the Imagin possessing him out of fear of Den-O's health; as Ryotaro encounters a former classmate nostalgic for the past.
Yuto Sakurai's past self appears before Ryotaro to tell him to not try to be so reckless in his pursuits again as a violent Imagin suddenly makes its move in the present.
Hana suspected that her future and Zero Liner have reconstructed, she asks young Yuto about what he knows. Then, two Yuto pass each other on the battlefield while a bad Imagin makes trouble.
After Ryotaro becomes arrested while trying to return Sieg's host, Hana tries to teach the troublesome Imagin what it means to be a real, responsible prince.
Ryotaro continues to attempt to assist the Zeronos of the present in protecting a contract holder from the Spider Imagin even as Yuto's future self keeps dragging him to another time.
After defeating Gaoh, Ryotaro's ability to fight as Den-O becomes complicated when three of the Imagin start to fade away due to the measures needed in the prior showdown.
A former suitor of Airi returns in hopes of winning her heart in the absence of the missing Sakurai, leading to Sakurai's younger self and even Ryutaros to respond.
As Den-O has trouble dealing with the Anthopper Imagin, Sakurai contemplates the need for the final Zeronos card and the permanent damage that will occur if finally used.
The Den-Liner crew discover an anomaly associated with the missing future as Hana suddenly transforms into a young girl. Meanwhile, the Kraken Imagin makes a contact with an old pianist.
Ryotaro works to try and figure out the mystery of the wandering piano player and what his true wish is before his Imagin can complete its desire. Yuto feels like he will go the same way as the pianist.
Fearful of Yuto's fate knowing of the truth of what happens to those who aren't remembered, Ryotaro decides to try to become strong enough to protect him and time.
As Ryotaro's dread on Yuto's fate is furthered with him becoming Zeronos again, he and the Imagin try to figure a way for him to transform in the past due to the mysterious future line throwing off their synchronization.
Ryutaros finds himself conflicted when his boss arrives to check on his progress, while he continues to feel the anger of trying to win Airi from Yuto.
With the Den-Liner running amok throughout time, the Den-Liner crew must figure a way to save the trains while dealing with Ryutaros' feelings after being manipulated by Kai.
While Ryotaro tries to figure out the true purpose of Yuto's interactions with both present and past actions, Kai decides to experiment in eliminating Zeronos in the past.
With the people of the world altered from Yuto's removal from time, Ryotaro tries to figure out how to bring him back while dealing with Kai's manipulations.
Shocked by his actions in the world without Yuto, Deneb tries his hardest to create connections so that his partner will not disappear with the usage of his Zeronos cards.
Discovering that the female contract holder's wish was for Yuto himself, Deneb continues to try and make things memorable in hopes of helping his partner make true lasting memories.
With the realization that the defeat of Kai may mean the departure of the Imagin, Ryotaro begins to try and prove that he can fight on his own without any assistance.
With Ryotaro continuing to deny the help of the Imagin out of fear of losing them, Momotaros decides to take a stand while the others deal with the stowaway Imagin in the King Terminal.
Ryotaro tries to find a way to travel back to the day his sister, Airi, lost her memory, in hopes that it would reveal the full truth regarding what happened to her and to her fiance Yuto.
With the shocking revelation of what really happened the day Yuto disappeared with Airi's memory, Ryotaro must piece together how it connects to his broken memory as the truth regarding the key to the Junction Point is revealed.
When Kai begins a multi-tier attack in order to eliminate Airi, both Ryotaro and Yuuto try to stop him, with a Imagin deciding to help in trying to make sure that the past and future is protected.
On their way back to stop Kai from killing Airi, Urataros takes over the DenLiner with several other Imagin, dumping Ryotaro at the moment where his missing memory is revealed.
Ryotaro returns to the present to confront Kai and bring an end to his mad reign of terror, even if it means an end to all Imagin, including Momotaros and his allies.
