While working late, Togusa gets a call from one of his colleagues from his days on the police force. It seems that he's uncovered something strange happening with the investigators in the Laughing Man Unit, a special task force formed to catch the infamous cyber criminal known only as the Laughing Man. But before he can meet with Togusa, he's killed in a car accident.

The Laughing Man returns! And, just as he did six years ago, he kidnaps the president of Serano Genomics without being detected. Section 9 arrives at Serano's house too late, and sets out to find him.