- Main article: Shinto Christian Mythology
Shinjuku was an orphan who was being attacked by 2 Kuro Akatsuki Soldiers who takes him to the Ka Boa Bu's Laboratory along with Grimlock and the Other Dinobots. Following a pain-based test, the restrained Shinjuku was approached by the Pilot of the MSN-20 Boulder Zaku who was an Izumo Soilder trying free Shinjuku but was caught by the Kuro Akatsuki Commander in his Apsalus Dragon, who offered to free Shinjuku in exchange for helping Cloud on reviving the Ten Tails by unlocking it's Chakra on the Tailsmen within Shinjuku's Chest. Grimlock proposed a counter-offer: grabbing the less than cautious Commander and using him as a projectile to smash the control console. Now free, Shinjuku was finally rescued by Kyoji Gekko who was simply takes Shinjuku as his Disciple while Grimlock and the Dinobots returns to Cybertron and made their way through the duplicate space-bridge tower Shockwave and his Insecticons had constructed, leaving a path of destruction and dead bodies in his wake. Shinjuku stood out as a genius — his talents, knowledge, and determination were considered by Paul Gekko to be that of a prodigy seen once in a generation. Shinjuku is a Close Friend of Riku. Shinjuku is a Childhood Friend of Reina. Riku, Shinjuku, Taiken, San and Tsuki became Team Kyoji before the Final Battle in Ka Boa Bu. After the Final Battle, Team Kyoji celebrated Kyoji's 200th Birthday at the White Angel.
- Shinjuku the Shinobi was named after the City in Tokyo.