Set one year after the fight between detectives Saya Toma, Takeru Sebumi, and Satoshi Chii. More confrontations ensues between the detectives at the Unidentified Crimes Unit of the Tokyo Metropolitan Police Department. Takeru Sebumi returns after taking a break due to his eye problems. Kenzo Ichiyanagi is appointed section chief, while Kotaro Nonomura is demoted. New member Shu Kikkawa joins the team.

Saya Toma is a female detective with an IQ of 201. Takeru Sebumi is a career detective with a distinguished background. They work on cases by postulating the "SPEC" of the unknown criminals and then deduce the criminal's unknown "SPEC" to make arrests. A mystery occurs when bodies are found on a cruiser in the ocean. Saya Toma and Ryo Kase of the Tokyo Metropolitan Police Department are brought in to solve the case.

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".

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".

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".