Though it suffers from an inconsistent and weak plot, and the presence of Jim Carrey, the strengths of Brad Silberling’s “Lemony Snicket’s A Series of Unfortunate Events” more than compensate for its faults. An eerily beautiful atmosphere, an uncannily talented pair of child actors, a mature wit and an unerring sensitivity make “Lemony Snicket” stand out among other children’s films.

Adapted from the first three books of a series by Daniel Handler (aka Snicket), the film follows the three Baudelaire children as they are shuffled from one inept guardian to the next after the death of their parents in a fire. To complicate matters, as Violet (Emily Browning), Klaus (Liam Aiken) and Sunny (Kara and Shelby Hoffman) move from house to house — including one bizarre abode filled with reptiles and another precariously suspended over the edge of a cliff — they are pursued by the sinister Uncle Olaf (Jim Carrey). Old Olaf tries his best to win guardianship of the orphans, so that he can kill them and take possession of the vast fortune they’ll inherit when they come of age. Fortunately for the children, Violet’s ingenuity, Klaus’s photographic memory and Sunny’s unusually sharp incisors are more than a match for the alternately sinister and oblivious adults who complicate their lives.

The film’s atmosphere is by far its most compelling aspect. Suffused with a beautiful moodiness, it is at once enchanted and dark. This is no brightly colored piece of juvenile film candy. Not since Tim Burton’s “Batman” has a filmmaker created a metropolis so darkly gothic as the timeless, unnamed world of “Lemony Snicket.” The skies are cloudy, the architecture is baroque and decrepit, and the denizens are unfailingly morose. The haunting score and Dickens-meets-Versace aesthetic beautifully complement the mood.

But the grimness that pervades the film only enhances its visual splendor. There is an aerial shot of a marsh swirled like marbled paint and a dazzling tour of a forest in which every surface is covered with bright moss and clover. “Lemony Snicket” may not be perfect, but it is visually sumptuous.

Browning and Aiken are perfectly cast to suit this beautifully mournful film. They are ethereally lovely, with pale skin and piercing eyes that are convincingly otherworldly. They also possess an unsettlingly precocious gravity that is sufficient to convey depths of woe (the cast of “Harry Potter” is surely jealous).

Carrey, however, is chronically unimpressive. Although he is gifted enough, he is unable to infuse his slapstick with enough malice to play the children’s homicidal uncle. His Olaf has too much of “The Cable Guy” in him to be truly threatening.

Similarly disappointing is the film’s storyline. Silberling toys with the idea of a “mystery” for the children to solve, but seems to lose interest providing any conclusive solution. This may be because the film is only an adaptation of the first three books in a series; after all, some loose threads had to be left dangling for future books (or, theoretically, movies). The viewer is left with a sense that nothing has really been deduced or explained.

But “Lemony Snicket” is nevertheless an intelligent film. The dialogue is blessedly free of cliche and sentimentality. And Silberling has a penchant for leaving deliciously subtle references lying around for older moviegoers. For a split second, we see the words “Damocles Dock” blazoned on a sign at the location of one of the many disasters that befalls the children; the excellent Meryl Streep, playing one of the children’s temporary guardians, shows the children an album full of pictures ostensibly of herself and her husband, who actually turn out to be 1920s explorers and photographers Martin and Osa Johnson.

“Lemony Snicket” could have easily been made into a much less admirable film in lesser hands. Thankful, Silberling refuses to rob the work of its more mature themes or aesthetics. He isn’t afraid to make the film almost unbearably melancholy at times, and he doesn’t degrade his child actors by portraying them as cute or scrappy. Instead, he enriches the film with undertones of loss and regret.

While the film is by no means too complicated or pessimistic for younger audiences, Silberling doesn’t feed us potty humor either. But it isn’t its childlike heart that makes it worth seeing; the refusal to shy away from heartache is what elevates the moody “Lemony Snicket” above its peers.