Less than a year after Geist activated the Death Force, which decimated most of Jerra's population, he has kept himself busy by dismantling the Death Force machines one by one. Most of the remaining human population have fled to a remote haven run by a warlord named Krauser. Krauser is another MDS unit, MD-01, who has a technology that hides his mobile fortress from the Death Force.

Kamen Rider OOO stars Shu Watanabe and Ryosuke Miura reunite in the first Toei Hero Next project, a sci-fi mystery about a traumatized former elite reporter named Tomoki Chino and a mysterious photographer with five personalities named Rei as they solve a mystery involving people who turn into stone and die. This case is also related to Tomoki's lover who died three years ago.

Geist (the main character) is MD-02, a Most Dangerous Soldier, genetically engineered to function as a killing machine, but every one of the MDS units went homicidally insane. As a result Geist was placed in suspended animation in a stasis pod orbiting the planet Jerra until it crashed several years later, awakening him and bringing him into another war on the planet.