When the lights come up on an eerily-lit Anne Frank marionette dictating from her diary on a bare stage, we knows we’re in trouble. What kind of perverse mind would dream up this utterly creepy creature?

The answer appears in the next scene and will dominate the show — Sid Silver (played by Mandy Patinkin of “The Princess Bride” fame), the novelist responsible for the publication of the famous diary who will spend the rest of his life artistically and personally obsessed with Anne. The play, based loosely on a true story, follows Silver through the publication of the original manuscript and the rejection of his own attempt to adapt the story to the theater. In the second act Silver continues his obsession in Israel, decades after he has promised his wife he will forget Anne.

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The show is often rather unpleasant to watch — we are disconcerted at the words of the famous young Holocaust victim, uncomfortable at Sid’s explosive outbursts at colleagues and loved ones and, of course, totally freaked out by the puppets.

The play also deals with issues of Jewish identity in a challenging manner. At one point, Silver’s friend and would-be supporter suggests the script’s ending is ineffective — the big Nazi showdown is superfluous to the emotional truth of Anne’s story. “Anne doesn’t have to be a Jew in relation to an enemy,” he explains to Silver, “She can just be a Jew.” This is a sentiment Silver absolutely does not understand in either his show or his life. His aggressive Jewish-obsessed rants, disdain for others, scathing self-criticism and general “holier-than-thou” attitude quickly get annoying, wearing patience thin for a lead character with whom it is hard to empathize, despite sympathy at his painful predicament.

Anne also solicits a surprisingly complex emotional response, especially considering her presentation in a theatrical mode generally considered most effective in upbeat children’s TV shows. This is certainly no Sesame Street, but Anne has all the spunk, clarity and unexpected manipulative cruelty that children often demonstrate. The production’s puppeteers do an amazing job bringing Anne and the other marionettes to life with a range of subtle motions.

The use of puppets also allows the fantastic cast to show off their vocal talent. In one scene, Silver’s wife (played, along with all other female roles, by the dexterous Hannah Cabell) wakes up and reaches for her husband to find Anne in the bed. The resulting dialogue quickly transitions from CREEPY to honest, wrenching and tender. For the only time in the show, Anne is voiced by Silver, occasionally visible in the dark behind the bed. Patinkin does a wonderful job bringing the puppet to life, illustrating a range of emotions and personalities in both Anne’s and, by extension, Silver’s characters. The fact that this scene, seemingly designed to make its audience as violently uncomfortable as possible, can pull itself off is a tribute to the artistry of the actors and this production.

Despite such talent, the show as a whole fails to coalesce effectively. As Silver’s wife and friends repeatedly ask when the obsession will end, the audience finds themselves asking the same thing — some episodes seem as superfluous as Silver’s climactic Nazis, with a similar capacity to distract from the real, simple, human truth of the story. Go if you’re obsessed with puppets, all those goddamn goy anti-Semites, or “The Princess Bride” — otherwise, not the Rep’s best.

Correction: Feb. 7, 2010

A photograph accompanying the review of “Compulsion” at the Yale Repertory Theater depicted the protagonist’s wife talking to the puppet of Anne Frank, not Anne Frank talking to herself, as the caption originally suggested.