Tired of writing riddles for children, Yamaoka Momosuke plans on gathering spooky and gruesome stories and publishing them in an anthology called Hyakumonogatari ("One Hundred Tales"). While researching these old myths and legends he comes across a mysterious trio who call themselves the Ongyou. They are detectives who are investigating the legends to reveal their truths...and bring those in the wrong to justice. Each time Momosuke meets the Ongyou he must face horrible truths and battle with his morals, but he's seeing things he shouldn't be seeing...

Professor Hershel Layton—renowned archaeologist, puzzle-solver, and extraordinary gentleman—and his young aspiring apprentice Luke Triton receive a mysterious letter from his former student Janice Quatlane containing tickets to an opera at the Crown Petone. They soon discover that it is no ordinary opera, but rather a devious game for the legendary Fountain of Youth—the giver of eternal life. However, this only scratches the surface of an unfolding mystery that the pair must solve together in order to survive. Despite being faced with complex puzzles and fervent competition, Professor Layton and his trusted assistant Luke never forget to uphold the standards of true gentlemen... and a true gentleman never leaves a puzzle unsolved.

The film's story centers on Musashi Miyamoto, one of the most famous swordsmen in Japanese history. He pioneered the Hyouhou Niten Ichi-ryuu style of two-sword fighting and wrote The Book of Five Rings, a book that has been compared to Sun Tzu's The Art of War for its insight on tactics and strategy.

"A man with arms which can kill people like puppets is not aware that he himself has already become a puppet." In this short hand-drawn silent animation, a wandering samurai learns this lesson firsthand. Along his travels, the samurai comes across a straw dummy at the base of a tree, with a sword lodged in its body. Upon drawing it out, the samurai learns that the blade is imbued with magic, and immensely powerful. The power comes at a price, though, and wielding the blade begins to slowly drive the warrior mad. He now has a choice to make: remain himself, or sacrifice his sanity for ultimate power?