The boy was reported missing from his Kips Bay home in the 13th precinct on Sept 26.
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A photo was distributed, and the NYPD received a tip that he was in the suspect's Bronx neighborhood.
Detectives from the Special Victims Unit went to the neighborhood and spotted the boy walking into his Gerard Avenue building with food.
Detectives started talking to the boy, who told them he was staying with "my friend Mike", authorities said.
Detectives said they went into the apartment at 6 a.m. Tuesday and found 31-year-old Michael Barreto living with a virtual studio, with multiple cameras pointed at his bed and lighting.
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He is suspected of filming sex acts with teens, and police are looking for more victims to come forward. Barreto is charged with the sexual exploitation of a child and possession of child pornography.
"I sat with Michael so many times there on that staircase, and I said to Michael you need to stop or you need help," one neighbor said. "He said the devil made me do it."
Barreto has three prior arrests, including a Sept. 7 arrest in the Bronx for acting in a manner injurious to a child, harassment and unlawful imprisonment.
Neighbors knew about his past convictions and prison terms and many, including children, said they still considered him a predator.
The NYPD transferred custody of Barreto to federal authorities. He will be arraigned in federal court in Lower Manhattan Wednesday.
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