警察官が連続して殺される事件が発生した。凶悪テロ、あるいは過激派の犯行なのか? 殺された2人はいずれも警察手帳をにぎりしめていた。コナンは小五郎とともに事件について聞き出そうとするが、白鳥刑事が放った一言は“Need not to know(知る必要のないこと)”。これは警察内部で使われる用語で、事件が警察内部に関わることを意味する。警視庁からの情報がない中、ついには蘭の命までもが狙われる!
The Persona Century Corporation has purchased nearly every parcel of land on earth. Dissension is not tolerated within the corporation's borders and those who oppose Persona are dealt with swiftly. Of those few places not yet under Persona's control is the free town of Kabuki-cho, also known as "The Dark Side of Tokyo". Within the town, under the leadership of a woman named Mai, is a small resistance group called Messiah. Into this world steps a man who takes the sobriquet of Kabuki-cho: Darkside. Sealed up in another dimension eighteen years ago by Persona Century, Darkside now returns to aid Messiah using his unique mystic power of renewal.