"Journal of the Mysterious Creatures" is a supernatural mystery anime that centers around a young researcher named Haruto Soma, who specializes in cryptozoology. The story begins with Haruto inheriting a mysterious journal from his late grandfather, a renowned cryptozoologist. The journal contains detailed entries about elusive and mythical creatures, many of which are believed to be extinct or purely fictional. Intrigued by the journal's contents, Haruto embarks on a global journey to investigate the existence of these creatures, uncovering secrets that blur the line between myth and reality.

The narrative is structured around episodic encounters with various cryptids, each tied to a specific region or cultural folklore. Haruto is accompanied by a small team, including Aya Fujimoto, a pragmatic biologist skeptical of the supernatural, and Kaito Takeda, a tech-savvy adventurer with a knack for uncovering hidden truths. Together, they navigate treacherous environments, decode cryptic clues, and confront both natural and supernatural challenges. The journal serves as both a guide and a source of conflict, as its cryptic warnings and incomplete entries often lead the team into perilous situations.

As the series progresses, Haruto discovers that the creatures documented in the journal are connected to a larger, ancient mystery involving a secret society dedicated to preserving the balance between humanity and the supernatural. This society, known as the "Guardians of the Veil," operates in the shadows, manipulating events to ensure that the existence of these creatures remains hidden. Haruto's investigations inadvertently draw the attention of the Guardians, forcing him to confront their motives and his own grandfather's involvement with the group.

The anime balances episodic storytelling with an overarching plot, gradually revealing the true nature of the journal and its connection to a prophecy involving the resurgence of a powerful, ancient cryptid. Themes of curiosity, the ethics of scientific discovery, and the coexistence of humans and the supernatural are explored through the characters' interactions and moral dilemmas. The series concludes with a climactic confrontation between Haruto and the Guardians, as he must decide whether to protect the secrets of the cryptids or expose their existence to the world.