According to a probable cause statement, Johnson and Lumpkin blamed each other for the child's injuries, which included severe burns on his face, neck, lip, arms and genitals; loose teeth; and deep cuts and ligature marks on his wrists.
The court documents say Lumpkin initially told police that Cortez was visiting relatives in Arkansas but subsequently acknowledged he had spent the 10 days before his death at the couple's Columbia home.
"Some gruesome injuries were inflicted," Boone County prosecutor Dan Knight said. "Cortez died a horrible death."
According to court documents, two unnamed witnesses told police that on June 16, they saw Cortez standing naked in the bedroom corner, his hands tied behind his back with duct tape. When Cortez tried to turn his head away from the wall, Lumpkin turned the child's head back at Johnson's direction, the documents said.
Police said they found blood stains in the couple's master bedroom as well as a harness fashioned from belts, duct tape and a restraining device made of a knotted rag and a telephone cord.
Police said Lumpkin told them that she left the home three times over the 10 days before her son's death but made no attempt to seek help. She initially was jailed on charges of endangering the welfare of a child.
Johnson fled Columbia for East St. Louis, Ill., after taking Cortez to the hospital the night he died. Federal marshals arrested him on a parole violation.
Lumpkin is being held on a $1 million bond. A public defender had not yet been assigned to her case.
Johnson's arraignment is set for Tuesday. No attorney was listed for Johnson on court documents filed Thursday.
Johnson is in the custody of the Missouri Department of Corrections. Boone County Jail operators said Johnson was at the Fulton Reception and Diagnostic Center. Calls there on Friday night went unanswered.
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