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Aaron Thompson pleaded not guilty today to multiple criminal counts, including those that accuse him of repeatedly abusing his children and causing the death of one them, his daughter Aaroné.

Thompson did not speak during his arraignment before Arapahoe County District Judge J. Mark Hannen.

Clad in slacks, a dress shirt and tie, he sat quietly next to his lawyer, James O’Connor, while Hannen advised him of his rights.

When Hannen asked Thompson whether he was ready to enter a plea, O’Connor rose and told the judge he was entering a plea of not guilty on behalf of Thompson to all of the 60 criminal counts returned by the Arapahoe County grand jury.

Among the charges Thompson faces are child abuse resulting in death; conspiracy to commit child abuse; accessory to a crime; false reporting to authorities; abuse of a corpse; concealing a death; and multiple counts of child abuse resulting in injury.

Aurora police have worked the case nonstop since Aaroné, then 6 years old, was reported missing by her father on Nov. 14, 2005.

At various times, Thompson and his common-law wife, Shelley Lowe, denied they had anything to do with the child’s disappearance.

In May 2006, Lowe died of an apparent heart condition.

A year later, in May 2007, the Arapahoe County grand jury returned the 60-count indictment against Thompson.

According to the grand jury, Thompson repeatedly beat Aaroné and shut her in a closet for hours — sometimes overnight — for wetting her bed.

On the night authorities believe she may have been killed, according to the indictment, Aaroné had wet the bed and was taken to the basement of their Aurora home, where she got “whooped,” which is how the seven other children in the house described their repeated beatings.

One child described how he was in bed and awoke from the sounds of Aaroné “getting a whoopin’.”

“He thought it was in the basement because he could hear her screaming,” the grand jury report said. “He heard the screams echoing through the vents in the basement. Aaroné stopped screaming at some point, and it went dead silent. He then heard Thompson say an expletive.

The next day or the day after, the indictment said, Lowe told the children that Aaroné had gone to live with her biological mother in Michigan.

Before Lowe died, she told her former boyfriend that Aaroné “just stopped breathing” and died in a bathtub, and that she and Thompson buried the child in a field, according to the grand jury report.

They had to get rid of the body, she said, because there was a scar on her back where they had disciplined her and Lowe feared that all the children would be taken away.

The grand jury alleged a pattern of continual abuse against the children in the Thompson household.

At least one other child was allegedly tied naked to a pole in the basement and was hit on his buttocks, legs and back with a baseball bat by Thompson.

Judge Hannen set a full day of motions for Sept. 3; a pre-trial hearing for Oct. 24; and trial for Nov. 3.

Howard Pankratz: 303-954-1939 or hpankratz@denverpost.com

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