According to the criminal complaint, R.J. died from ingesting a "combination of fatal drugs through breast milk" and is being charged with criminal homicide.
Jones' attorney, Louis Busico, said that Jones "absolutely, unequivocally loved that child" and never intended to harm him.
According to an affidavit, Jones told investigators that about 3 a.m. April 2, she heard R.J. crying.
He had been primarily breastfed, Jones said, but she had recently started using formula because she worried that he wasn't getting enough milk and wasn't sleeping. She was too tired to make a bottle of formula, according to the affidavit, so she decided to nurse him. She then dozed on and off for a few more hours.
Before her husband, Vincent McGovern, left for the day, he made R.J. a bottle and left it with Jones. She remembers feeding R.J., putting him back in his bassinet around 6:30 a.m. and going back to sleep.
In the affidavit, Jones said she woke up about an hour later and panicked when she saw that R.J. was pale and had bloody mucus coming out of his nose. Jones and her mother, who also lived in the house, called 911 and began CPR.
R.J. was taken to a hospital by ambulance and pronounced dead by 8:30 a.m.
According to the Bucks County Coroner's Office, the autopsy revealed traces of methadone, amphetamine and methamphetamine were found in the infant's blood and contributed to his death.
The affidavit further noted that the examiner who performed the autopsy said "R.J. ingested the combination of fatal drugs through breast milk."
According to the affidavit, Jones told the investigators that she had been prescribed methadone since pregnancy to help manage her addiction to opioid painkillers, but there is no mention of other drugs.
Investigators say they tested the bottle last used to feed R.J., as well as the can of formula, and found no traces of illicit drugs.
Since her arrest, Busico said, his client is "completely in a state of depression." He added that the charges and arrest kicked Jones when she was already down, dealing with the death of her child.
When asked about amphetamine or methamphetamine drug use by Jones, Busico would not comment.
At Jones' preliminary hearing on Wednesday, Deputy District Attorney Kristin M. McElroy argued that the child died because Jones had taken methamphetamine and amphetamine, "which had no business being inside that baby," according to a press release from the Bucks County District Attorney's Office,
"We are not alleging that this was an intentional killing of this baby," McElroy said, "but it certainly was reckless to know these drugs were in your body and continue to breast feed."
The criminal homicide charge was upheld and Jones now awaits a formal arraignment on September 28. Busico said Wednesday he was not surprised by the decision.
"The judge's ruling today is no surprise given the low burden on the government," he said. "Samantha is not criminally responsible for her son's death -- this is a fact pattern in search of a crime."
Through her attorney, Jones declined to speak with CNN.
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