Touma Kamijou meets two girls in Academy City's back alleys. One is Ayu Mitsuari, a lady of Tokiwadai Middle School with the Mental Stinger power to control people's minds. The other is Seria Kumokawa, a mysterious genius high school girl who can control people's minds without any power. Kamijou is at the mercy of those girls, but those peaceful times do not last long. That kind time is torn apart by a gigantic creature that towers over them: a dragon. Who is the Biohacker who created it, controls it, and freely gives it the power to fight? Why is that giant creature pursuing Ayu Mitsuari? Touma Kamijou enters Academy City's deep darkness to protect the girls. It all happened one year ago. It is the summer of Touma Kamijou's third year of middle school. This is an untold story different from the time he spent with Misaki Shokuhou. Touma Kamijou's starting point begins here. (Source: Kadokawa, translated)

Toaru Majutsu no Index SS: Biohacker-hen was included with the limited-edition Blu-Ray/DVD volumes of Toaru Kagaku no Accelerator.