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Mariah Woods sparked a nationwide Amber alert when she disappeared from her room after her mother, Kristy Woods, put her to bed on Nov. 26.

Police, the FBI and community members came together to scour the area where the 3-year-old North Carolina girl vanished, as previously reported by Dearly.

However, the frantic search for the missing girl came to a tragic end when her body was found in a remote North Carolina area in the water on Saturday.

Her mother's live-in boyfriend, Earl Kimrey, was arrested not long after.

While Mariah's mother, Kristy, was pleading for daughter to be brought home, her biological father, Alex Woods, flat-out questioned the idea of a kidnapping. Per WCTI, he said:

Someone just walked right up in there, grabbed the 3-year-old out of the bed and she didn't cry, she didn't scream? Nobody heard anything? Four people in the house, two adults and two kids, someone just comes up and snatches the baby and walks out?

Now, court documents are shedding light on why he felt that way.

WFMY reports the father accused Kimrey of sexually abusing Mariah and physically abusing her two brothers in documents filed for his custody battle with Kristy.

Alex claimed the man accused of murdering the 3-year-old girl used a belt to beat her brothers, causing a bloody nose on one of the boys after he was hit in the face.

The document also stated Mariah's mother knew Kimrey was sexually abusing her daughter, according to JDNews.com.

One of Mariah's brothers said his mother knew what her live-in boyfriend was doing to her daughter, and she allegedly “failed to protect the juveniles from exposure to sexual abuse,” according to the documents.

Alex told WCTI he was granted custody of their children after their mother was investigated by Child Protective Services, but he had not seen them since last year, which was not by choice.

Kimrey was hit with a long list of charges after Mariah's body was found, including concealing of death, obstruction of justice, second-degree burglary, felony larceny and possession of stolen property.

According to WECT, Kimrey walked into his first court appearance on Monday wearing a bulletproof vest. Onslow County Sheriff Hans Miller said:

We were concerned for his safety and we had to protect him. We didn’t want anyone to take justice into their own hands.

He is being held on $1.01 million bond, with his next court date set for Dec. 18.

Watch coverage of the story below, via WECT.