In the year 2201, one year after the Yamato saved Earth from radioactive contamination, a new threat emerges. The Yamato makes its final journey to save the Earth from this new threat. Earth has almost recovered from the battle against Gamilus, and reconstruction has expanded to the other planets. When former Yamato crew-mates discover a strange, garbled message that seems to be coming from a white comet headed towards Earth, they hijack their old space fortress and begin a new battle.

2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a "Cosmo Reverse System" at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the "Gatlantis," and that its leader is the Gutaba expeditionary force commander who calls himself "Goran Dagaamu of Thunder." The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the "Flame Direct Attack Cannon" that can transcend space. Yamato was able to retreat, but ends up getting lost, and finds itself in a strangely colored irregular dimension. The crew decides to turn off the engine on the ship, and explore a mysterious planet. In order to collect information, Kodai, Kiryū, Sawamura, Niimi, and Aihara land on the planet. What they saw when they arrived was a ship that was not supposed to be there. Dagaamu chases after the traces of Yamato's warp, and also reaches the strangely colored space. The planet on which Yamato landed was in fact what Dagaamu had been looking for all along.

Shoutarou Hidari, a hard-boiled private investigator from the Narumi Detective Agency, lives for the sake of protecting the peace in the city of Fuuto alongside his inquisitive partner, Philip. One fine night, Shoutarou encounters a mysterious woman named Tokime, who is soon linked to several cases of homicide and theft. Shoutarou's investigation leads him to people using "Gaia Memories"—memory units similar to thumb drives holding vast amounts of data—to turn into formidable beasts called "Dopants." While the majority of Gaia users were put down by the detective team in the past, a number of them still remain, posing a great threat to public safety. Once more, Shoutarou and Philip, Gaia users on the side of justice, must fight as Kamen Rider W—the renowned hero safeguarding Fuuto—to eradicate the nest of villainous Dopants, all while uncovering Tokime's true identity and confronting the long-forgotten past.

Mushi-uta's story takes place in the near future. Ten years before the story's opening, strange insect-like creatures known as "Mushi" began appearing. The Mushi are able to consume peoples' dreams and thoughts in return for supernatural powers. At the end of episode one, protagonist Daisuke "Kakkou" Kusuriya encounters a young girl named Shiika Anmoto. The two, in time, become quite close. However, unbeknownst to Kakkou, Shiika is an escapee from a secret prison known as GARDEN where those posessed by the Mushi, known as the Mushitsuki are held. GARDEN's military force, the Special Environmental Conservation Executive Office, dispatches its finest killer to track down Shiika. However, they are faced with resistance from the Mushibane resistance organisation, led by the secretive "Ladybird."