When she woke up, her baby was gone, she told police, according to the San Bernardino County Sheriff’s Department.

The reported kidnapping in Yucaipa, about 30km east of San Bernardino, spurred law enforcement to dedicate “all available resources” to try to find the infant.

Media reporting on the story led to an outpouring of concern from the public, who gathered with parents Rebecca and Jake Haro in the following days to join the search.

“Please don’t hurt him,” Rebecca Haro said to KCAL/KCBS through tears, holding up a “Missing Kid” flyer showing a photo of Emmanuel, along with the parents’ names and phone numbers. “Protect him and just bring him back to his parents that love him.”

But police say inconsistencies in the couple’s story arose within 24 hours.

And just over a week later, Jake Haro, 32, and Rebecca Haro, 41, were arrested at their home in Cabazon on charges of murder and making a false police report.

According to a criminal complaint, Emmanuel was killed sometime between August 5 and August 14, a nine-day period leading up to their call to police reporting his disappearance.

The Riverside County Public Defender’s Office did not immediately respond to a request for comment. An arraignment for the pair is set for September 4.

Officials spoke to offer further details on the case and correct the record of the reported kidnapping.

“It’s appropriate to have a press conference because it was the defendants in this case who had a press conference first, and they did so in order to tell the public, the media, and ultimately law enforcement that their child had been kidnapped, when in fact that’s not what occurred,” Riverside County District Attorney Mike Hestrin said.

As for baby Emmanuel, the child’s remains have not yet been found, but investigators have a “pretty strong indication” of the location, Hestrin told CNN during the press conference.

“The filing in this case reflects our belief that baby Emmanuel was abused, victim of child abuse, over time, and because of that abuse he succumbed to those injuries,” he said.

Parents had pleaded for child’s return

After reporting the kidnapping to police, the Haro parents spoke to KCAL/KCBS pleading for the baby’s return and explaining their version of what happened.

“I took him out of the car seat and I laid him on the chair, and I had his diapers right here, and someone said ‘Hola,’ and I couldn’t even turn and that was just – I don’t remember nothing,” Rebecca Haro, sporting a black eye, said through heavy breaths.

“He was a healthy baby, he was crawling, he was kicking, he was playing with his toys,” Jake Haro told KABC. “Whoever took our son, please give him back.”

Behind the scenes, officials became skeptical, and notably for a missing child case, authorities did not send out an Amber Alert. In law enforcement interviews, Rebecca Haro was “confronted with inconsistencies in her initial statement and declined to continue with the interview,” the sheriff’s department said.

Investigators also served several search warrants at their home, used K9s in the search and obtained surveillance video, the department said. Authorities said they could not rule out foul play.

Days after the initial kidnapping report, the investigation reached another conclusion.

“Based on the evidence, investigators determined a kidnapping in Yucaipa did not occur,” the sheriff’s department said. “It is believed Emmanuel is deceased and the search to recover his remains is ongoing.”

The parents were arrested last Friday, August 22, and were booked into separate Riverside County jails, officials said. There are no other suspects. Each is being held on $US1 million ($1.5 million) bail.

“The circumstances surrounding this investigation are tragic and we will continue to search for Emmanuel,” Sheriff Shannon Dicus said in a statement. “I trust our justice system will hold the parents accountable.”

There is “some level of cooperation” with the suspects, San Bernardino County Sheriff Shannon Dicus said. “Our job is to follow every lead.”

Two days after his arrest, investigators – accompanied by Jake Haro and cadaver dogs – searched for baby Emmanuel off the freeway near Gilman Springs Road in Moreno Valley, the department said. The infant was not located.