Eiji Hino, the user of the OOO Driver, is fighting a group of Mole Imagin when the monsters escape by jumping into a young boy named Naoki and traveling through time. Kotaro Nogami, the young Kamen Rider New Den-O, arrives aboard the time-traveling DenLiner with his partner Teddy and his squad of boisterous Imagin, Momotaros and his companions, to pursue them. Eijis partner, the greedy Greeed Ankh, convinces him to board the train, and they all travel back to November 11, 1971. Kotaro defeats the Imagin, but during a scuffle over some Core Medals, Ankh unknowingly drops a single Cell Medal, which is found by a soldier from the evil organization Shocker.

When the group returns to the present day of April 1, 2011, they discover a horrifying alternate reality. Shocker has successfully conquered the entire world, merging with other evil organizations from across the Kamen Rider timeline to eliminate resistance. Humanity is nearly extinct, and shockingly, the original heroes, Kamen Riders 1 and 2, now serve as Shockers most powerful enforcers after being brainwashed. The heroes learn that the dropped Cell Medal caused this disaster. Shocker scientists used a stolen Core Medal to create a Shocker Medal, which absorbed Ankhs lost Cell Medal to birth the all-powerful Shocker Greeed, a monster that defeated and enslaved the Double Riders, preventing any future Kamen Riders from ever being born.

Determined to fix the timeline, Kotaro and the DenLiner crew return to 1971 to retrieve the medal. However, a series of mishaps further complicates the past, including Ankh dropping another medal and the involvement of three orphan childrenNaoki, Mitsuru, and Shigeru. The children befriend the Riders and the Kamen Rider Scouts, a group of children training to fight Shocker. The heroes manage to destroy the original Cell Medal, but Shocker uses the chaos to create the Shocker Greeed anyway, attacking the DenLiner. During a desperate battle, Teddy sacrifices his physical form to protect Naoki and the Riders.

Back in the conquered present, the Riders are captured and scheduled for public execution. As the crowd gathers to watch, the tide turns. Shigeru returns Eijis transformation gear, and the brainwashed Kamen Riders 1 and 2 break free from their control thanks to a sympathetic Shocker scientist. The citizens, inspired by decades of heroism, rise up to protect the Riders from the Shocker foot soldiers. One by one, nearly every Kamen Rider from the 40-year history appears to join the final battle, alongside other legendary heroes like Kikaider, Inazuman, and Zubat. As Eiji unlocks a new form, the Tamashii Combo, he leads the charge against the monstrous final form of Shocker's Great Leader. After the villain is finally destroyed, the timeline is restored. In a final twist, the scientist who saved the Double Riders is revealed to be the older version of the boy Naoki, who was left behind in the past and grew up to become Mitsurus father. With history corrected, Eiji bids farewell to Kotaro and the DenLiner as they depart for their next adventure.