Bryce McIntosh is accused of killing Noah McIntosh, who was last seen more than a month ago after his mother dropped him off at the father's apartment.
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Bryce appeared in the Riverside County courtroom a day after he was reportedly in a hospital. The 32-year-old appeared unshaven and wearing an orange jumpsuit as he spoke with his court-appointed public defender.
Minutes later, his attorney entered the plea of not guilty to the charge of murder with the special circumstance of torture on his behalf.
The child's mother, Jillian Godfrey, also remained in custody Wednesday. She and the victim's father were both initially arrested on child cruelty charges. Bryce pleaded not guilty to those charges.
MORE: Document shows disturbing details in Noah McIntosh case
Noah McIntosh case: Corona dad charged in son's murder allegedly bought acid, 32-gallon trash can, bolt cutters, court document shows
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A court document revealed disturbing details of the murder case, including investigators' belief that Bryce purchased acid, bolt cutters, a 32-gallon trash can and other items before the boy went missing.
Detectives have determined through their investigation that the 8-year-old little boy, who would have turned 9 this past Sunday, is likely dead.
In Corona, the community continues to remember Noah with a sea of blue ribbons.
"We've heard many stories like that in the past, of children being abused like that or missing," said Corona resident Martin Narvason. "People are realizing we have to step in and start protecting these kids."
The maternal grandfather of Noah says the family is planning on holding a memorial service out of state with just family. He says without a body, there is no closure.