Ultraman Saga opens with a powerful apocalyptic vision of Tokyo, buildings destroyed and the city seemingly devoid of life. We are soon introduced to the Earth Defense Force (EDF), Team U (played by members of the female idol group AKB48). They and a group of young children and the last survivors on planet Earth after the world was invaded by the evil Alien Bat, the rest of the human population having been abducted.

Hiromi appears on the outside to be a mature, resilient girl, but on the inside she feels like she's falling apart. She is having troubles at home mainly because of her parents wanting to separate. Her dog, Junkers, tries to comfort her in ways no other dog can. You see, he can talk and grant her 3 wishes.

Namiko Morita, who lived in Otaru, moved to this area with her husband, Yutaro, and opened the brewery "Morita Brewery". Eventually, they succeeded in this business and lived happily while raising three children. However, in August 1945, the situation changed completely due to the Soviet invasion of Manchuria.

In 1999, an enormous meteor crashed onto Earth carrying extraterrestrial creatures known as Worms within it. These creatures took on the identities of real humans and then killed them. In order to counter this new threat, ZECT was formed, who in turn created the Masked Rider System to combat the Worms. The battles lasts over seven years, depleting Earth's resources and turning it into a barren wasteland. By present time, power struggles in ZECT have caused a new group, known as Neo-ZECT, to be created. Souji Tendou, a man weilding the Kabuto Zector, decides to sell his power to either ZECT or Neo-Zect for unkown reasons.

A low-ranking yakuza is given the mission to kill a high-ranking yakuza from a rival group. Wanting recognition, he accepts the assignment, only to meet an enthusiastic office lady.

Arata Kagami seeks to get the Hyper Zecter just like Souji Tendou, so he tries to emulate Tendou. Once he realizes that he has to be himself, the Hyper Zecter appears and allows him to transform into Kamen Rider Gatack Hyper Form.

Tatsuhiko relocates from Shinjuku to Yokohama, where he comes into conflict with Masaki Taki, CEO of the local scout company.

20 years after the events of the series, in a world where humans and Worms coexist, what is the purpose of the reactivated ZECT? New Kamen Riders appear.