Not long after, Yonatan vanished.

He did not return to class, nor to his after school program. Although his family had been the subject of a half-dozen reports by the Los Angeles County Department of Children and Family Services, social workers had no legal ability to inquire about him, the Times reported.

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Yonatan’s stepfather, Jose Pinzon, believed the boy was living in Mexico. The boy’s mother, Veronica Aguilar, allegedly told him so, and said the same to other people who wanted to know his whereabouts.

That was the story until August 2016, when Aguilar came to Pinzon with tragic news: Yonatan had died. Pinzon, who said he had not seen the boy in several years, figured she would be going to Mexico for the funeral.

Instead, she opened the closet door.

Inside was the 11-year-old’s body, wrapped in a blanket and surrounded by medicinal cups. His hair was falling out, his nose was plugged with foam, and pressure sores covered his tiny frame. He weighed just 34 pounds.

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“I took care of the problem by ruining my life,” Aguilar allegedly told Pinzon.

Details of the harrowing saga were culled from Los Angeles County Juvenile Court records and published Thursday by the Times.

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Aguilar, 39, has been charged with murder and child abuse and is being held on $2 million bail, according to the Los Angeles County Sheriff’s Department. She has pleaded not guilty and faces 15 years to life in prison if convicted, according to KTLA.

Aguilar’s defense attorney told the Times: “My client is innocent until proven guilty.”

Why Aguilar allegedly kept Yonatan hidden for so long remains a mystery — perhaps one that will be explored in her criminal case — but police said she was so crafty that for three years Pinzon may not have realized that he and his stepson were under the same roof, according to the Times.

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Sometime in 2012, Aguilar pulled Yonatan out of school, apparently because she was offended by questions from social workers, the Times reported.

As the couple and their four children moved from house to house, the Times reported, Aguilar kept the boy locked in closets, sedating him with liquid sleep medications. When Pinzon would go out for groceries, Aguilar would always ask him to pick up purple-colored “syrup,” records show — something Pinzon reportedly found confusing because they were tight on money.

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At the time of Yonatan’s death, the family was living in a one-bedroom house in the Los Angeles neighborhood of Echo Park, according to the Times. Two children shared a bedroom and a third child slept in a shed outside, while the couple slept in the living room. Her children appear to have known what she was doing, but concealed it from their stepfather, the Times reported.

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It was Aug. 22 when Aguilar allegedly told Pinzon the truth about Yonatan. After seeing the boy’s body, Pinzon ran out of the house and called police from a 7-11, according to the Times.

When detectives arrived, they interviewed Pinzon and the children in the same room. Pinzon exploded when he realized the children knew, reported the Times, which described the exchange from records:

“How can you do this to me?” he asked. One of the children replied: “You were always at work, so you didn’t know.” Pinzon then started crying. “I carry a photo of him in my wallet,” he said, according to the records. “I’m the only one that cared for him.”

A public memorial was held for the boy at an Echo Park church last month, according to KTLA. Among the speakers was Moses Castillo, the lead detective in the case.

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“Yonatan, I pledge to you that we will continue to tell your story in hopes that similar cases do not repeat again,” he told people who had gathered to remember the boy.

Pinzon also recalled his relationship with the boy.

“He’s still alive for me,” Pinzon said, “because I carry him in my heart.”