A 12-year-old Detroit boy who went missing for a dozen days before turning up in his own basement is out of the hospital but hasn't been allowed to see his father and stepmother, police say.

Charlie Bothuell V was evaluated by doctors Wednesday night after he was found in a shared utility and storage area of the multiple-unit condo near downtown Detroit, said police spokesman Sgt. Mike Woody.

The Detroit News reported Friday that the boy had been released to the custody of his biological mother and that Michigan Child Protective Services had removed a four-year-old boy and a 10-month-old girl from the home as an investigation into possible abuse continues.

The stepmother, Monique Dillard-Bothuell, was taken into custody after a gun was found in the home during a search. She is on two years’ probation for a misdemeanour gun charge, the News reported, citing an unnamed source.

Dillard-Bothuell appeared in court on Friday when she was ordered to wear the tether and a judge set personal bond at $5,000. She's due back in court July 11. Mark Magidson, a lawyer representing Dillard-Bothuell and her husband, said her arrest was "highly disingenuous" and he's advised her not to talk to investigators unless he's present.

After the hearing, the elder Bothuell told reporters: "I have something to say, but I can't right now."

Investigators weren't allowing the boy to have contact with his father or stepmother, as they focus on the circumstances surrounding the boy's disappearance and his surprising recovery.

"Finding Charlie alive and well was obviously a big win, not just for us — the department — but for their family as well. So, we're all very excited about that," Woody said.

The elder Bothuell, a nurse, reported his son missing June 14. The boy had been working out about 9 p.m. ET, went to the restroom and never returned, Bothuell told police.

He seemed surprised by the discovery of his son when he was informed of it during an interview on HLN's Nancy Grace show.

Local media reported that police were taking a close look at both the boy's father and stepmother.

Searched 3 times

A family member, however, said Charlie's father was innocent and not involved in his son's disappearance.

"My son has nothing to do with this," Charlie's grandmother Pierette Bothuell said. "I know my son. I don't feel he had anything to do with this."

Police found Charlie in a small backroom in the basement. Detroit Police Chief James Craig said the police had searched the house on at least three occasions, including the very spot where Charlie was later found.

Local media said detectives believe the boy may have been in and out of the basement.

Missing Boy Detroit

Charlie Bothuell IV becomes emotional arriving home after the Detroit Police Department found his missing 12-year-old son, Charlie Bothuell V, in the basement of his home in Detroit, on Wednesday. (Kimberly P. Mitchell/Associated Press)

"We're not certain at all that Charlie was here during those visits," Craig said. "Not certain at all. The question is how could we miss."

Police stumbled across the boy apparently hiding behind boxes and a large plastic drum on Wednesday afternoon. There were some bedding, soda bottles and cereal nearby, but police have said they do not believe the boy was in the basement area the whole time

"It wasn't like he was living down there," Woody said. "It didn't give off that vibe.

"It wasn't situated in a way that would lead you to believe that he was being hidden or held captive and tortured and that sort of stuff."

The boy's father, who made tearful television pleas for help, said he had no idea his son was in the basement.

With files from CBC News