Ms Fraser, 23, was nine months' pregnant when she vanished from Pyramid Hill in the state's north after visiting a friend's house about 9.30pm on June 20, 2009.
No body and no criminal charges, her family has waited more than 13 years for answers.
Coroner Katherine Lorenz finally shed light on what may have happened to Ms Fraser on Thursday, as she handed down her findings on the disappearance.
She concluded Ms Fraser, who lived with a mental impairment, had died and her death was caused by another person.
Ms Lorenz said Peter Jenkinson, the potential father of Ms Fraser's unborn son, had something to do with her disappearance and death.
"I have had regard to the circumstantial evidence before the court, which satisfies me to the required civil standard that Mr Jenkinson was involved in her disappearance in some way," she told the court.
Ms Fraser died "very shortly" after receiving a phone call from a Leitchville phone box, just before midnight on June 20, she said. Her phone then pinged two towers, in Patho and Leitchville, in the early hours of June 21.
Mr Jenkinson, who was excused from giving evidence to the inquest as it may incriminate him, was likely the person who called Ms Fraser from the phone box.
Following the call, he was involved in transporting Ms Fraser from her Pyramid Hill unit to an area near Patho and then near Leitchville, where her phone pinged towers in those areas, Ms Lorenz said.
Phone records indicated Mr Jenkinson was awake and not at home when Ms Fraser's phone moved between those locations, she said, and he had given differing accounts as to his whereabouts that evening.
Additionally, she found he had lied to police about his sexual relationship and communications with Ms Fraser, and said they were likely together around the time the baby was conceived.
"I accept the submissions of the parties that there is insufficient evidence for me to conclude to the requisite standard that Mr Jenkinson was responsible for Krystal's death," she said.
"However, there is no evidence that excludes Mr Jenkinson as a person who may have been involved in her death."
About a month before Ms Fraser vanished, she said Mr Jenkinson stopped calling Ms Fraser from his mobile phone or landline and started calling her from a Leitchville.
He did this to "in order to conceal his contact with her before she disappeared," the coroner said.
Mr Jenkinson has denied any involvement in Ms Fraser's disappearance and said he did not speak to her using the Leitchville phone box on June 20, in submissions to the inquest.
Ms Lorenz has referred the matter to the Director of Public Prosecutions, as she believes an indictable offence was committed in connection to Ms Fraser's death.
She said it was regrettable the inquest could not resolve how Ms Fraser died, nor the location of her and her baby's bodies.
A Victoria Police spokeswoman said police were reviewing the coronial findings and a $1 million reward remained on offer for anyone with information that could lead to successful prosecution.
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