Set in New York City, the story concerns Anise Murphy, a high schooler who is fascinated with her classmate Siva (real name Jake Rang), a beautiful boy who works as an actor and model and has a reputation for being unapproachable. Anise takes a chance and declares to Siva that she wants to be friends with him, which he accepts, much to her joy. Shortly after, however, she discovers that he has a twin brother called Cipher (real name Roy Rang) and that the two lead a life of switching places for their convenience. The twins challenge Anise to figure out who is who within two weeks, and she moves in with them to better study them. If she can figure it out, they'll reveal to her why they constantly switch places.
There is a 1989 OVA by Magic Bus based on the manga called Cipher the Video. Rather than a straight attempt at an adaptation, it's a rather unorthodox piece of animation consisting of several disparate scenes set to popular American music of the time such as Phil Collins and Kenny Loggins. For authenticity reasons, it's also dubbed entirely in English by (non-professional) native speakers instead of Japanese.
- Always Identical Twins: The Rang twins are so identical that it's almost impossible to tell them apart, and they even regularly perform Twin Switches without anyone suspecting it.
- The Bet: The twins make a bet with Anise that if she can tell who is who between them after two weeks, they'll tell her why they make a lifestyle out of switching places, and if she fails she can never tell anyone their secret.
- Big Applesauce: New York City is the main setting, and where Anise and the twins live. Its landmarks are prominently displayed, including, yes, the Twin Towers, which are even used at several points to symbolize the twins themselves.
- Eagleland: A rare manga that's set in America and has a cast of mostly American characters. The author is a self-professed America-phile, so the depiction of the country is very loving and accurate to reality (if a bit idealized).
- No Celebrities Were Harmed: According to the author, Siva's (and by extension Cipher's) appearance is based on musicians Tom Bailey and Limahl.
- Twin Switch: Siva has a twin brother Cipher, who regularly takes Siva's place in his daily life; the real Siva goes to school while Cipher-as-Siva is the one who goes out to do the actor/model work (due to the real Siva having a scar). The twin not playing "Siva" that day hides at home and doesn't even answer the phone or the door to keep up the masquerade.
- Twin Test: The entire plot is one big twin test with Siva and Cipher finally revealing to Anise why they so often switch between each other when she figures it out.