Justin Laurens Stein, 33, has pleaded not guilty to murdering Charlise on or around January 12, 2022, at Mount Wilson, in the Blue Mountains west of Sydney.
The nine-year-old was found dead inside a barrel with two gunshot wounds, to her head and lower back, after an intensive four-day search of the area.
Charlise's mother, Kallista Mutten, left the Mount Wilson property in the early hours of January 13, driving Stein's Red Holden Colorado ute, a NSW Supreme Court trial was told on Wednesday.
The pair were in a relationship at the time, with Ms Mutten travelling alone to a nearby reserve where she sent text messages to friends that prosecutors say are consistent with her belief the child was missing.
"Bring back my car now. I'm saying this only once," Stein says in one voicemail played to the court.
"If you don't bring it back I'm going to hurt you as well as everyone else.
"I've got me f***ing guns and i'm going to kill you."
Sounding increasingly angry and frustrated, Stein threatens to tell police Ms Mutten had taken her daughter.
"Have fun - between everything I can put on you, you're going down dog," he says.
Ms Mutten returned to the property with Stein's car shortly after, the court was told.
Stein's lawyer argued earlier this week it was Ms Mutten who had shot the girl, and that he had only helped to dispose of her body.
Police were led to the girl's body by using Google location data stored on Stein's phone, the jury was told on Wednesday.
The data indicates on the same day he verbally threatened Ms Mutten, Stein travelled to at least three separate boat ramps across Sydney - at Rose Bay, Drummoyne and Windsor.
CCTV images captured of the trip showed Stein towing a boat, with what prosecutors allege is a barrel containing Charlise body in the back tray of his ute.
Phone data and CCTV footage tracks Stein's movements for close to eight hours, before the data showed he returns to the Blue Mountains near the Colo River, stopping at two locations for roughly five minutes each.
At one of the locations detectives found traces of sand and scrape marks and were able to visually locate the barrel with Charlise's body down a steep hill towards the river.
Soon after Stein returned from allegedly dumping Charlise's body, Ms Mutten called triple zero to report the girl missing.
In a recording of the call played to the jury, Ms Mutten tells the operator the last time she saw her daughter was two nights earlier after she left her alone with Stein.
"She was here and I wasn't here, my partner was here ... during the morning she was sort of sick, so she was sort of lethargic and I was two-and-a-half hours away," Ms Mutten said in the call.
She told the operator Stein had left Charlise, who he claimed was sick, with a woman who had come to do a valuation of the 12-acre Mount Wilson property owned by his mother.
"He asked if she could mind her while he went and got me ... he didn't want her in the car because she'd been throwing up," Ms Mutten said.
"When we got back they were gone."
Crown prosecutor Ken McKay SC earlier told the jury Charlise being sick and remaining with the property-valuer was one of two lies Stein told Ms Mutten about what happened to her daughter.
He would later suggest the nine-year-old might have been taken by people from his criminal past.
Officer in charge of the investigation, Detective Sergeant Bradley Gardiner, began giving evidence on Wednesday and is expected to remain in the witness box for the rest of the week.
