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Japan is an Asian country consisting of a string of islands off the northeast coast of the continent. The Japanese civilization is one of the oldest and most historic in the world, with a rich cultural history. Its largest city and capital is Tokyo.

Thomas Cahill, founder of the Tomas branch of the Cahill family, settled in Japan after many years of searching for his sister, Katherine, without success. He married a Japanese woman, Keiko, and fathered a son, Hiyoshimaru Cahill, who unified Japan under the name Toyotomi Hideyoshi. The Tomas branch has continued to keep a strong presence in the country, with a stronghold in Tokyo in addition to the branch's main stronghold inside Mount Fuji, the tallest mountain in Japan. Additionally, branch leaders selected Tokyo as the host of the 1964 and 2020 Summer Olympics, and also hosted the Winter Olympics in the Japanese cities of Sapporo in 1972 and Nagano in 1998. The purpose behind these strongholds is unknown, as no other Cahill branches are known to have strongholds or secrets in the country. However, the Vespers had a stronghold in Nagasaki, at Hashima Island.

Janus agent Fidelio Racco visited Japan and forged two swords, later named Rufus and Remus by Dan Cahill, which Racco used to hide the Janus Clue Tungsten. Another notable Janus, Akira Kurosawa, was Japanese. Madrigal agent Erasmus Yilmaz spent several months in Japan with his mother while running from the Vespers and learned ninjutsu, and another Madrigal, Fiske Cahill, studied subduction zones during a visit to the country. A third Madrigal agent, Hope Cahill, visited the country with her husband, Arthur Trent, while hunting for Clues.

During the Clue Hunt, at least three teams, Teams One, Three, and Seven, visited Japan while searching for a Clue, Gold, hidden by Hideyoshi.

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