Watch “Guillermo del Toro’s Pinocchio” — a stop-motion marvel now in theaters and available Dec. 9 on Netflix — and it soon becomes apparent that del Toro has undercut Collodi’s thesis, carving out a paean to thinking for yourself.

“Pinocchio” was born as a violent, scare-’em-straight morality tale with a central lesson: One way or another, kids, you shall be shaped into obedient creatures. Through many iterations since, including Disney’s iconic 1940 animated feature, the lying boy puppet must forever learn to fall in line, with dire consequences at every turn when he doesn’t.

Del Toro, though, has no problem going against the grain.

“Even when I was a little child,” del Toro says during a recent Zoom call, he resisted “the idea of obedience being a virtue. Disobedience is a virtue.”

Running counter to the traditional moral of Pinocchio’s story became an operating principle on the new film. The director wanted his “Pinocchio” to bear his cinematic signature as distinctly as “Pan’s Labyrinth” and “The Devil’s Backbone” — two other films in which children fight back against cruel forces during wartime in Europe. The former landed the writer-director his first Oscar nomination. More recently, del Toro’s 2017 film “The Shape of Water” won four Oscars, including best picture and director, and this year, his “Nightmare Alley” garnered four Academy Award nominations.

Many of the animated musical’s textured storytelling choices emanated from the decision to condemn blind obedience, says del Toro, who worked closely with two animation veterans: co-writer Patrick McHale (“Adventure Time,” “Over the Garden Wall”) and co-director Mark Gustafson (“Fantastic Mr. Fox”).

“Disobedience has a certain value to it — it’s how we learn who we are as people,” Gustafson says by phone.“To question authority is something that we need to do.” In this “Pinocchio,” personal development is centered on how characters react to outside forces rather than how they are molded by them.

Review: “Guillermo del Toro’s Pinocchio”: Disney it ain’t

Political and religious allegory run deep, as “Guillermo del Toro’s Pinocchio” becomes a World War II-set tale of physical and spiritual fathers, as well as the fatherland. Pinocchio’s paternal figures — including Geppetto, who also carves a towering wooden crucifix for the town church — seek to stay in the good graces of either civic leaders or the Mussolini government.

Although this “Pinocchio” is set in the past, with SpongeBob voice actor Tom Kenny as a comical Benito Mussolini, del Toro laces his film with a currently resonant narrative commentary on fascism. Beware the authoritarian string-pullers and the puppet dictators alike.

“Disobedience now is more urgent than ever,” says del Toro. “Dogma or ideology are really hollow to the human spirit because they do not strengthen it. They just tell you, ‘Accept this unquestioned.’” The point is made: Pinocchio might have a hole where his heart should be, but is the unthinking servile person any less hollow?

And the choice of Il Duce’s Italy as the film’s setting was made for heightened effect. “I wanted very much for Pinocchio to land in a very hollow time in which everybody behaves like a puppet except the puppet,” del Toro says. “Even Geppetto is popular because he does what everybody wants and he obeys.”

Del Toro describes himself as a lapsed Catholic, and underscores how his films reflect his religious upbringing. It was important to him that his Italian-pine Pinocchio is “related to the same woodcarver who carved the Christ” for the church, del Toro says. As a story of fathers and sons, “Pinocchio gets basically crucified visually on the screen and resurrects three times and offers his own life to redeem others.”

Ultimately for del Toro, though, “Pinocchio” comes down to the relationship between parent and child, with all its flaws and imperfections and possibilities for redemptive love. The film even became biographical. “It’s a bit painful in a good way for me, because I’ve seen where I’ve failed or where I was failed,” he says. “You end up repeating the mistakes your father made.”

Once again, the director chose an interpretation different from previous iterations of “Pinocchio.” What if it wasn’t Pinocchio who needed changing, but those around him? “If Geppetto is going to be this sanctified, benign little old man,” he says, “then it’s not a story about fathers and sons — it doesn’t have emotional reality.”

And what if the son could redeem the father?

“This is a ‘Pinocchio’ in which Geppetto learns from Pinocchio, in which the cricket learns from Pinocchio,” the filmmaker says. “But Pinocchio basically learns to bring love and acceptance to [their] lives. That’s why he doesn’t have to transform into anything to be loved.” The big-hearted puppet need not conform to others’ definition of real.

“He brings so much light and love into this world that he is accepted for who he is.”