Like The Seven Percent Solution and The West End Horror, The Canary Trainer was published as a "lost manuscript" of the late Dr. John H. Watson.

In "The Adventure of Black Peter", an original Arthur Conan Doyle Holmes story from 1904, Watson mentions that his companion recently arrested "Wilson, the notorious canary-trainer, which removed a plague-spot from the East-End of London."

This Wilson (who figures prominently in the Adrian Conan Doyle pastiche "The Adventure of the Deptford Horror") is not related to the eponymous character of Meyer's novel.

The Canary Trainer describes Holmes's adventures during "The Great Hiatus" of 1891–1894, when (according to the Sherlockian Canon) he was traveling the world, trying to escape the minions of Professor Moriarty; in Meyer's The Seven-Per-Cent Solution, however, a different impetus is given for this period, and this alternate scenario is maintained here.

The bulk of the novel is a first-person narrative, in which Holmes recounts a visit to Paris, where he played violin for the Palais Garnier and became entangled with a mysterious "Phantom".

He learns that all minor mishaps are attributed to the Ghost, a spectral personage who haunts the Opera's labyrinthine passageways, sometimes appearing to ballet dancers wearing an evening suit but without a head.

All goes well until the prima donna soprano, La Sorelli, falls ill and is replaced by Irene Adler, a past adversary known for her ability to outwit Holmes.

His admiration for her provokes uncertain emotions, largely foreign to his calculating nature—but he soon realizes that torment is secondary, when the opera rehearsals subject him to her incomparably beautiful singing.