Mysteries are revealed like the words "Simple Plan," "Third Secret of Fatima" and also the mysterious white man which are all mentioned in the movie "SPEC: Heaven".

High school student Saya Toma lost her parents and younger brother in an airplane accident. Detective Akio Kondo came and told her "your family has a high possibility that they were killed by people who have spec." That was the first time she heard of "spec". 6 years later, Saya Toma, who has never forgotten what the Detective said, decides to become a detective. She returns to Japan after receiving training by the FBI in the United States. Saya Toma is assigned to work unsolved cases in the Public Security Bureau. Meanwhile, because of Satoshi Chii's scheme, Juichi Ninomae considers Saya Toma his parents' enemy and tries to push her to the edge. Satoshi Chii's scheme has also caused Saya Toma and Juichi Ninomae to forget that they are brother and sister. The siblings are headed to a life-staking fight. A girl named Maho Ueno becomes involved in their fight. To protect Maho Ueno, Saya Toma uses "spec".

The story takes place on a world 100 years in the future, a few years before Lisa and Lorna joined eX-D organization. The world where people drives computer-controlled electrically powered "AI cars" which automatically take you where you want to go. However, one AI car mysteriously start to run amok. Now Nina and Rei, as the main driver for ex-D organization have to solve the mystery behind the AI car with evil plot and trap awaiting for them...

A wealthy broker, his loyal butler, and a poor street seller all see their social positions change in a twist of fate.