The Ape Who Guards the Balance begins in 1907 in England where Amelia is attending a suffragettes' rally outside the home of Mr. Geoffrey Romer of the House of Commons. It seems Romer is one of the few remaining private collectors of Egyptian antiquities, and a series of bizarre events at the protest soon embroil Amelia in grave personal danger. Suspecting that the Master Criminal, Sethos, is behind their problems, the Emerson Peabody's hasten to Egypt to continue their studies in the Valley of Kings where they soon acquire a papyrus of the Book of the Dead.

As with past seasons, however, their archaeological expedition is interrupted. The murdered body of a woman is found in the Nile. Ramses, Radcliffe, and Amelia all have their theories as to the origin of the crime, but their own lives might soon be at stake if the cult of Thoth and their ancient book is, indeed, involved.