恐怖分子在一间教堂里散播病毒，导致俄罗斯东部一座城市完全消失。同样的噩运即将降临日本，日本警视厅严阵以待，并请18岁的天才黑客高木藤丸（三浦春马 Haruma Miura 饰）协助参与其中。藤丸的父亲也是警察，原本负责这起案件，后因卷入误杀事件而被通缉。恐怖组织的折原麻弥（吉濑美智子 Michiko Kichise 饰）以生物老师的身份进入到藤丸所在的高中，并监视着藤丸。为了保护妹妹小遥生命安全，藤丸不得已答应了恐怖组织的要求盗取发电厂管理员密码给对方。在百货公司里，致命的bloody—x病毒怀疑被小丑散播，警视厅出动所有人力，为求保住东京市，差点让所有人命丧当地。幸好藤丸及时发现病毒是假的，虚惊一场。但当所有人都暂时放下心来时，恐怖组织已经开始踏出真正的第一步。
Bloody Monday，是所有死去的人最后说出的话，也是最大的秘密与阴谋。

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".