Jun Honganji is the Chief of the Special Investigations Division. He appears to be a typical incompetent management level person who does little more than to please his superiors and does nothing more than keep tabs on everyone in his department, particularly how he tries to have trouble-free days. He is the one who assigns Kiriko to watch over Shinnosuke, who is constantly skipping work and lazing off somewhere. He is an avid believer in divination and fortune-telling, and his necktie will be in the lucky color for that day. After Shinnosuke transforms into Kamen Rider Drive in front of many civilians, Honganji reveals that he is a longtime friend and supporter of Krim Steinbelt and has long been aware that Shinnosuke was chosen to become Kamen Rider Drive. He also reveals that he is personally responsible for establishing the Special Investigations Division to serve as the base of operations of Kamen Rider Drive and his support team within the police department. It is also revealed that Honganji is actually a very astute and perceptive police officer, with his goofy, incompetent, and trouble-fearing attitude only a clever facade. Along with establishing and keeping the Special Investigations Division intact, his eager pleasing of his superiors has always been a front to dig for information regarding the Global Freeze event from the upper levels of the police force. He was also responsible for revealing Shinnosuke's identity as Kamen Rider Drive to the mass media, having judged that doing so would protect Shinnosuke from the Roidmudes. After the Special Investigations Division is disbanded, Honganji keeps rising in the chain of command until finally becoming the Deputy Superintendent General of the Metropolitan Police Department.
Honganji eventually receives a Mass-Produced Mach Driver and Tokujo-Ka Key from Rinna Sawagami, to become the first user of the Mass-Produced Kamen Rider Mach system, dubbing himself Kamen Rider Jun. However, it is ultimately revealed to still be a prototype, leaving Honganji open to the effects of the Roidmude's time-freezing abilities.
In the film Super Hero Taisen GP: Kamen Rider 3, Honganji is one of a few people mostly unaffected by the changes to history by Kamen Rider 3, as he still leads the Special Investigations Division with Rinna Sawagami and Kyu Saijo. After Kiriko reveals to him that the timeline has been altered, leading him to help keep Kamen Rider Black safe from Shocker surveillance. He is killed when Cheetahkatatsumuri discovers Kamen Rider Black's location, but is brought back to life when the timeline is restored to normal.