GoGo Sentai Boukenger vs. Super Sentai is a direct-to-video tokusatsu movie. The movie celebrates the 30 year anniversary of the Super Sentai Series.
The movie starts with Time Demon Chronos meeting with High Priest Gajah on getting rid of the Boukengers while obtaining three Gōdom Engines. As they plot, a mysterious figure watches above them. Afterwards, the Boukenger, excluding Bouken Silver, were summoned to battle some Karths. After their battle, they see Gajah and Chronos, with Chronos sending the Boukengers to a different dimension. Eiji was alerted of the situation, but before he could set out to rescue the other Boukengers, a mysterious figure named Aka Red, who describes himself as the embodiment of the fighting spirit of all Red Rangers, meets him and gives him the Super Sentai Address Book, which lists information on every Super Sentai member. He opens it to find Tsubasa Ozu, a.k.a. Magi Yellow from Mahou Sentai Magiranger.
Eiji tries to talk to Tsubasa during his boxing match, but ends up getting ejected from the side of the ring since he was interfering with his match. Next, Tetsu, a.k.a. Deka Break from Tokusou Sentai Dekaranger, is undercover trying to negotiate with Alienizers when Eiji interrupts. Eiji tries to acknowledge Tetsu's background as Deka Break, but Tetsu beats him up and sends him out the window to maintain his cover. Elsewhere, at the Duel Bond site, Chronos shows a time device, a reverse flowing hourglass, to Gajah, which when augmented to a Godom Engine enable him to revive one of the Three Sorcerers, past Super Sentai villains whose magic caused the greatest harm to the Earth. Chronos would set another up at the Matrix ruins with Gajah remaining to welcome the second Sorcerer while Chronos installed the final device at the countryside. In Chronos' time prison, the Boukengers find out they were blocked of their technology and they meet up with Hikaru, a.k.a. Magi Shine, also from Mahou Sentai Magiranger.
Eiji then receives a call through his Go Go Changer from Asuka, a.k.a. Abare Black from Bakuryu Sentai Abaranger, all the way from Dino-Earth while taking care of his daughter. He tells Eiji that Aka Red contacted him, but the connection to Earth is weak since the power of the dimension door is weak as well. Even contacting him was hard through the Go Go Changer. He loses connection to Eiji after a few minutes. While Chronos set up his time devices, Hikaru talks to the Boukengers about Chronos and the Boukengers are introduced to Smokey, although at first mistaking him as precious. Eiji then tries to meet Nanami, a.k.a. Hurricane Blue from Ninpuu Sentai Hurricaneger, before her rehearsal, but is blocked by security and many fans. In a desperate attempt to catch Nanami's attention, Eiji shouts out "Hurricane Blue," which Nanami is surprised by.
Chronos was then successful in summoning Meemy, from Mahou Sentai Magiranger, who meets up with Chronos. In frustration, Eiji throws out the Super Sentai Address Book and decides to battle Meemy and Chronos on his own. After Eiji is overpowered, he was rescued by Hurricane Blue, Abare Black, Deka Break and Magi Yellow. However, the various Super Sentai warriors repeatedly get in each other's way and Meemy and Chronos were able to escape. In the time prison, Akashi reveals that he has Zuban with him. Tsuetsue from Hyakujuu Sentai Gaoranger was then revived and welcomed by Gajah.
At SGS, Eiji receives a message from Akashi concerning Chronos. The Super Sentai warriors then promised to help Eiji rescue the rest of the Boukengers and meet Aka Red while the time prison holding the Boukengers and Hikaru is slowly disappearing. Chronos and the other villains found the last hourglass tipped over, with the final Sorcerer missing, when they were attacked by the Super Sentai warriors. As the time prison started to disintegrate, Sakura analyzed and concluded that the clock with root-like designs in the wall was the key to their escape. The Boukengers and Hikaru then utilize the Magi Lamp Buster's Smoky Shining Attack, accompanied by Zuban, on the clock in the wall. Although this does not damage the clock at all, it causes another root-like clock in the real world to appear. Aka Red orders the other warriors to destroy the clock while he takes care of the villains, transforming into Magi Red and Gao Red respectively, and frightening both Meemy and Tsue Tsue in the process; for both respective villains, Magi Red and Gao Red were their worst enemies. As Aka Red fights off the villains, the others succeed in freeing the Boukengers and Magi Shine from the alternate dimension.
The Super Sentai warriors and the villains face off, with the Sentai warriors getting the upper hand until Furabiijo from Ninpuu Sentai Hurricaneger interferes after "taking a walk". But with all three Sorcerers present and accounted, Chronos fuses them all into the Staff of the Three Philosophers, his intended goal from the start. With the power of the staff, Chronos enabled himself to grow to gigantic proportions with new golden armor. The Boukengers countered with Ultimate Daibouken and Siren Builder, but Chronos proved too powerful for both the mecha and were defeated. In a last-ditch effort, the Boukengers summoned Dai Voyager, which was almost defeated by Chronos as well. Aka Red, sensing the danger, came back into the action, becoming a vessel to power up Dai Voyager using the Spirits given by the remaining Super Sentai warriors, enabling Dai Voyager to access its Burning Legend Form. Burning Legend Dai Voyager went on to defeat Chronos with the special attack, 30 Super Sentai Soul (an energy attack powered by the Super Sentai warriors of the past), and sent the released sorcerers back into the afterlife. After their victory, the Boukengers and the other Super Sentai warriors return to the SGS headquarters, and then parted ways. The Boukengers, however, would not have time to relax, as they receive another call from Mr. Voice concerning another Negative Syndicate on the move. The movie ends with Aka Red watching over the Earth in outer space, going into a deep sleep until he is needed again.