“Anomalisa” is the story of Michael Stone, a British-born author living in the states. He isn’t a glamorous figure: He writes about customer service, and his current book tour includes a stop in Cincinnati, Ohio. Michael smokes and drinks too much, but he has a bigger problem. In his mind, everyone looks and sounds the same, from his cabbie at the airport to his wife at home. At his hotel, however, Michael discovers an anomaly — Lisa Hesselman, an eager-to-please fan whose face and voice stand out from the crowd.

That’s exactly the kind of morose, surreal premise you’d expect in a film written by Charlie Kaufman, whose credits include “Being John Malkovich,” “Adaptation” and the relatively upbeat “Eternal Sunshine of the Spotless Mind.” Kaufman’s protagonists tend to be self-involved, oversensitive types who start out unhappy and get worse.

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“Anomalisa,” however, is different. It isn’t upbeat, but it isn’t thoroughly depressing, either. It’s a cautionary tale, and a useful one, about what we rightly or wrongly perceive as love.

“Anomalisa” also is made entirely with stop-motion animation — rare, if not unprecedented, for an R-rated drama. If the idea of animated figurines having awkward sex sounds kind of amusing, well, it is, but no more so than if real people were going through the motions. The animation, by Starburns Industries (whose junior partner, Duke Johnson, codirected with Kaufman) is astoundingly detailed and expressive. Thanks also to Joe Passarelli’s hazy cinematography, “Anomalisa” perfectly captures the weird ennui of time spent inside a midmarket hotel.

Making this film even odder, and more haunting, is the three-person voice cast. David Thewlis and Jennifer Jason Leigh (both excellent) play Michael and Lisa, while Tom Noonan (best known for 1986’s “Manhunter”) is credited as Everyone Else. Noonan literally plays every other man, woman and child in the movie — a performance surely unprecedented in cinema. It’s Noonan who drives home the creepy, depressing sameness of Michael’s world, in which only Lisa’s voice can be truly heard.

With its spooky atmosphere and wrenching ending, “Anomalisa” won’t be to everyone’s taste. It’s an anomaly in itself, unlike any other movie you’ve seen.