Now, police have charged Freund and A.J.'s mother, JoAnn Cunningham, with five counts of first-degree murder, and a host of other crimes, in the death of their son. It’s a disturbing development in a case that captured national attention and prompted a search effort that included the FBI and more than a dozen police departments.

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“A. J. is no longer suffering, and his killers have been brought to justice,” said James Black, the police chief in Crystal Lake, where the family lived.

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At a Wednesday news conference, Black glanced at the ceiling and spoke straight to A.J.: “We know you are at peace playing in heaven’s playground and are happy you no longer have to suffer.”

On Thursday, a judge set a bond for $5 million for each parent, the Northwest Herald reported.

They’re facing the murder charges, along with counts of aggravated battery, aggravated domestic battery and failure to report a missing child. Freund was also charged with two counts of concealment of homicidal death.

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Both Freund and Cunningham provided investigators with evidence that led them to A.J.'s body, hidden in a remote, rural area in nearby Woodstock, Black said.

Early Wednesday, the Chicago Tribune reported, police officers and evidence technicians were spotted leaving the family’s house, taking with them a shovel, a large tub, paper bags and a mattress. They also removed a dog, which a neighbor identified as a brown boxer named Lucy.

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In the days leading up to the arrests, police trained their investigation on the home, saying they had no reason to believe A.J. had been abducted. That was when, police said, Cunningham stopped cooperating with authorities. Her attorneys told the Tribune they advised her to cease communications with police once it appeared she was a suspect.

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Authorities had been familiar with the Freund home for years. A.J. lived there with his parents and his younger brother, who was placed in the care of the state’s family services department after A.J. went missing. Officers who visited the residence described a squalid, unkempt interior, according to a batch of redacted reports that local police released this week.

After one visit, an officer wrote that conditions were not up to "an acceptable standard of living with two young children living at the residence . . . I observed it to be cluttered, dirty and in disrepair.” Windows were broken, and dog feces and urine covered the floors, the report said. In the boys’ bedroom, the smell of feces was “overwhelming.”

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On other occasions, police observed that the house had gone without electricity for days and that one of the children had a “large bruise on his right hip,” which, police were told, may have been caused by the dog. One report describes suspected drug use by guests living in the house’s basement. A woman told police that she thought the guests were using heroin and said she had found a syringe on the kitchen floor.

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The Tribune reported that family services has been involved with A.J.'s family since he was born in 2013, when doctors found opiates in his system.

If they were released after posting bond, both parents would be required to avoid contact with anyone under the age of 17 and surrender firearms, the Herald reported.

Alex Horton contributed to this report.