When Vallejo police announced to the world that the abduction of physical therapist Denise Huskins was an elaborate hoax she cooked up with her boyfriend, investigators were sitting on evidence that could have led them to the real culprit in the sensational 2015 kidnap-for-ransom.

The failure devastated the couple. It led to a $2.5 million settlement from the city. It could figure into the prosecution of the kidnapper, Matthew Muller, which heads to court this week.

And, according to court records and interviews, it was easily preventable.

A day before the disastrous announcement, as Huskins lay shackled by a bicycle lock to a bed in South Lake Tahoe — where she said Muller raped her twice after snatching her from her boyfriend’s Mare Island home — police in Vallejo received leads that they grievously mishandled.

These clues came in the form of missed phone calls placed from an unrecognized number to Huskins’ boyfriend, Aaron Quinn, who was being grilled by police about her disappearance, records show.

Investigators traced the calls to a prepaid phone purchased from a Target store in Pleasant Hill, and they later viewed surveillance images of a man — allegedly Muller — buying the phone. Investigators also traced the calls received by Quinn’s phone to a location in South Lake Tahoe just a stone’s throw from where Huskins was being held at Muller’s parents’ vacation home.

Now Playing:

But instead of seeing the outlines of Muller’s crime, and dispatching resources to catch the dangerous offender, Vallejo police saw a fabrication. It appears they thought the man captured on camera in Target was either Quinn or an accomplice.

So when Muller dropped off Huskins at her family’s home in Huntington Beach after keeping her captive for two days, Vallejo police disregarded her story and called the episode “an orchestrated event” and a “wild goose chase.”

Huskins and Quinn were dragged through the mud. Muller remained free to strike again — and he did before he was caught months later, prompting Vallejo police to privately apologize to Huskins and Quinn.

“Police were going to disregard any facts that contradicted their theory, and that’s a tragedy,” said Dan Russo, Quinn’s lawyer. “The consequence of that is we know this guy was free to do a home invasion and traumatize another family. It’s really sad. It’s really pathetic.”

The saga took another dramatic turn last week when Muller, 41, was brought from a federal prison in Arizona to Solano County to face state charges of kidnapping for ransom, rape, robbery, burglary and false imprisonment. The Harvard-educated but now disbarred immigration lawyer and onetime Marine has already pleaded guilty to the kidnapping in federal court, earning a 40-year prison sentence.

A magistrate is allowing Muller, who now claims he’s innocent, to represent himself at a preliminary hearing scheduled for Tuesday. The Solano County district attorney’s office has subpoenaed Huskins and Quinn, both 33, meaning Muller may cross-examine his victims.

“This guy is unstoppable,” said Huskins’ attorney, Doug Rappaport. “There are very, very few that need to be locked up for life, but he’s one of them.”

Chief Deputy District Attorney Sharon Henry, who is prosecuting Muller, said the mistakes by investigators early in the case were “absolutely not a factor” in her decision to subpoena Huskins and Quinn. Often, prosecutors rely on police testimony rather than putting victims on the stand in preliminary hearings.

What remains to be seen is whether the strength of the case may be affected by the initial lapses of Vallejo police as well as the FBI.

The ordeal began around 3 a.m. on March 23, 2015, when at least one person sneaked into Quinn’s two-story home on Kirkland Avenue on Mare Island, threatened the couple with a squirt gun made to look like a pistol, bound and drugged them, forced Quinn to listen to instructions on headphones, and vanished with Huskins stowed in the trunk of Quinn’s Toyota Camry, which was soon abandoned.

When Quinn came to hours later, he called police and reported what had happened.

But even as Quinn begged officers to help find his girlfriend, investigators quickly focused on him as a suspect, his attorney said, interrogating him for hours, taking his phone and clothing, extracting blood samples and giving him a polygraph test. They thought his story was just too far-fetched in its horror.

During the grilling, Vallejo police Detective Mathew Mustard told Quinn “that they did not want to hear anything else about any claimed intruders, and that they knew that Quinn had really killed Huskins,” attorney Kevin Clune, who represented the couple in a lawsuit against police, wrote in court papers.

Agents from the FBI’s Fairfield office got involved the day after the abduction, as Muller sought to communicate and secure a $17,000 ransom. At 12:24 p.m., The Chronicle received an email from the kidnapper that contained an audio recording of Huskins recounting the day’s news and offering personal details only she would know.

“My name is Denise Huskins,” she said. “I’m kidnapped, otherwise I’m fine. Earlier today, there was a plane crash in the Alps, and 158 people died.” The newspaper turned the message over to police — who dismissed it as part of the hoax.

Meanwhile, the kidnapper couldn’t get through to Quinn. It wasn’t until that evening, eight hours after the proof-of-life message was sent, that investigators discovered the simple reason: Quinn’s phone was set to airplane mode, Russo said.

When they switched the phone back to regular mode, it showed two missed calls from an unknown number. The calls had arrived at 8:31 and 8:33 p.m. the day Huskins was abducted, according to an FBI affidavit.

Police traced the number to a prepaid wireless TracFone purchased three weeks earlier at the Pleasant Hill Target store. Target gave the FBI a photo of the buyer, a “light-skinned male, with dark hair, medium build,” the affidavit states. Both Muller and Quinn are white, with brown hair and medium builds.

It’s unclear from the records exactly when investigators saw the photo, when they traced the calls from the burner phone to South Lake Tahoe, and what they did with the information. Vallejo and FBI officials have long declined to comment in detail.

But the South Lake Tahoe lead, placing the TracFone near Muller’s parents’ home, could have been critical. Muller had been a suspect in three home-invasion attacks in Mountain View and Palo Alto in 2009 and 2012 that had remarkable similarities to the Huskins kidnapping.

Muller dropped off Huskins in Huntington Beach on the morning of March 25, 2015, and she immediately called police, telling them of the kidnapping and rapes.

But then, within hours, came the hastily prepared news conference, during which Vallejo police Lt. Kenny Park said that Quinn’s account of the kidnapping had been “such an incredible story, we initially had a hard time believing it.” He lamented the “wasted” resources put into the investigation.

Russo said the FBI was equally to blame for its role behind the scenes. The couple’s attorneys allege that the feds had a conflict of interest, because the lead agent in the case, David Sesma, had once been in a “personal relationship” with Quinn’s ex-fiancee, whom Muller identified as his intended target, rather than Huskins.

Privately, a law enforcement official told one of Huskins’ lawyers to watch the 2014 film “Gone Girl,” in which the title character fakes her kidnapping, to understand the police theory of the case, Clune said.

Huskins and Quinn remained under a cloud for months, though The Chronicle continued to receive emails from the purported kidnapper, who was shocked and angry that police doubted he was real. Then on June 5, 2015, Muller committed a home invasion in Dublin — he later pleaded no contest to the crime — and left his cell phone behind after the resident fought him.

Police reported that they traced the number to Muller and found him — along with a mountain of evidence in the Mare Island kidnapping — in South Lake Tahoe, in the same home where he had held Huskins and called Quinn.

Evan Sernoffsky is a San Francisco Chronicle staff writer. Email: esernoffsky@sfchronicle.com Twitter: @EvanSernoffsky