Mr Hughes told the court that it was the Crown case that Ms Paepaerei's then partner, Joshua Scott Homann murdered her and then crashed through an upstairs window fleeing the scene.
Ms Paepaerei's body was found by a young relative soon afterwards, but her unborn baby could not be saved.
Mr Homann is on trial for the 37-year-old mother's murder in a Sydney court where a large contingent of the victim's family gathered for the opening day.
The court heard that Mr Homann, who has pleaded not guilty to murder, had been taking methamphetamine at the time.
Both Mr Homann and Ms Paepaerei were ice users during the two years of their de facto relationship, but she had stopped taking the drug ahead of giving birth to her baby.
Mr Homann's barrister Peter Lang told the trial that his client was suffering from mental illness at the time of the death and that "this is not a case of domestic violence".
Crown prosecutor Mr Hughes told the court that before she died Ms Paepaerei had been living at a Chester Street townhouse in Mt Druitt with Mr Homann and "the pair had regularly used methamphetamine otherwise known as ice".
"[Ms Paepaerei] had stopped using illegal drugs in anticipation of the birth of her child," he said.
On the night of September 21, 2015 there had been young relatives coming and going from the house.
Mr Hughes said that two teenage boys arrived back at the two-storey house around midnight.
One of the boys allegedly saw Mr Homann at the top of the stairs yelling "shut the f***ing door" and "you f***ing, f***ing c**ts".
The two boys then allegedly heard a loud banging from upstairs and the sound of breaking glass followed by an alarm sounding from the accused's black Holden Commodore.
They then saw the Commodore reversing at speed from the driveway of the townhouse.
One of the youths yelled out, "Josh, someone's f***ing stolen your car."
When he rushed upstairs and turned on the light he saw Ms Paepaerei lying on the ensuite floor. The teenager raced down the stairs and rang emergency services.
In a triple-0 call played in court, the 16-year-old was heard sobbing and crying as he told the emergency services that Kirralee Paepaerei was dead.
Relatives cried as they heard the teenager's heartbreaking call, saying over and over that Ms Paepaerei was dead and begging "please hurry, please help".
But as the triple-0 operative asked him if it was possible that Ms Paepaeri might be still alive, he repeated four times that she "is dead" and "dead on the floor".
The young man described how he had discovered Ms Paepaerei's body in the upstairs ensuite of the house they shared and first thought she was playing a joke.
"I reached over and turned on the light," he said. "I found [Ms Paepaerei]. She was just laying there. I thought it was a joke at first. I was just tapping [Ms Paepaerei] and telling her to wake up.
"I looked at her neck and I knew straight away."
The emotional phone call included the teenager giving clear directions about what had happened and that Mr Homann had "jumped out the window".
His anguish and grief clearly heard in the phone call caused both male and female relatives to sob in court.
The trial heard that Mr Homann turned up at nearby Mt Druitt police station six minutes after his car was caught on neighbour's security camera leaving the Chester Street house.
Mr Hughes told the court that Mr Homann leant over the counter and said someone had broken into his house and tried to stab him.
"Someone came into my house and tried to kill me. I jumped out the window and drove straight here," Mr Homann is alleged to have told police.
Forensic tests would later reveal he had low levels of methamphetamine in his bloodstream.
Mr Hughes said it was the Crown case that Mr Homann did not drive straight to the police station and that diluted blood in the townhouse ensuite suggested "some washing away" of evidence.
A pullover top belonging to the deceased was later found outside in a garbage bin.
Near the bloodstained knife and large metal rod and blood spattered walls upstairs, "no evidence was found consistent with there being an intruder", Mr Hughes said.
He said that Mr Homann had later told psychiatrists that he suffered hallucinations from heavy ice use and had once cut into one of his ears and attended a mental health facility.
But it would be the Crown case that Ms Paepaerei "died at the hands of the accused and the accused alone".
The trial before Justice Lucy McCallum continues.
