Prosecutors announced new charges against a man who kidnapped and sexually assaulted a Northern California woman, which was originally thought to be a hoax, and has become known as the “Gone Girl” kidnapping.

Matthew Muller, 47, the man who abducted Denise Huskins in Vallejo in 2015, is now being charged in two home invasion cases from 15 years ago.

Muller broke into women’s homes in Palo Alto and Mountain View in 2009, with the intent to rape them, according to the Santa Clara District Attorney’s Office.

Thanks to a new lead and advances in forensic DNA testing, the Santa Clara County District Attorney’s Office, along with Palo Alto and Mountain View Police, were able to ID Muller in the cases. 

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Muller’s DNA was found on straps he used to bind one of the victims in one of the 2009 cases, the DA’s office said. 

Muller now faces two felony counts of committing sexual assault during a home invasion for the 2009 crimes. If convicted, he faces life in prison, officials said. 

“The details of this person’s violent crime spree seem scripted for Hollywood, but they are tragically real,” District Attorney Jeff Rosen said. “Our goal is to make sure this defendant is held accountable and will never hurt or terrorize anyone ever again. Our hope is that this nightmare is over.”

In the early hours of Sept. 29, 2009, officials said Muller broke into a woman’s Mountain View home, attacked her, tied her up, made her drink a concoction of medications, and said he was going to rape her. After the victim, who officials said was in her 30s, persuaded him against it, he suggested the victim get a dog, then fled.

Less than a month later, on Oct. 18, officials said Muller broke into a Palo Alto home, where he performed the same routine and bound and gagged a woman in her 30s. He then made her drink Nyquil and began to assault her, before being persuaded to stop. Muller gave the victim crime prevention advice, then fled.

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Denise Huskins and Aaron Quinn appear at a news conference with attorney Doug Rappaport (left) in San Francisco, Calif. on Thursday, Sept. 29, 2016. Huskins and Quinn were victims in the bizarre Vallejo kidnapping case in March 2015. Matthew Muller has pleaded guilty to kidnapping Huskins. (Paul Chinn/The San Francisco Chronicle via Getty Images)

Both cases were investigated at the time and went unsolved.

Muller gained national attention six years later as the subject of “American Nightmare,” a Netflix documentary series that chronicles his 2015 “Gone Girl Hoax” kidnapping of Denise Huskins from Vallejo and her harrowing 48 hours in captivity. 

On March 23, 2015, Muller broke into a Vallejo home, where he drugged, and tied up Huskins and her boyfriend. He kidnapped Huskins, brought her to a cabin in South Lake Tahoe, and sexually assaulted her. Two days later, Muller drove his victim to Southern California and released her. 

The Vallejo Police initially believed the invasion and kidnapping were a hoax orchestrated by her boyfriend, Aaron Quinn, a twist that the media deemed a “real-life ‘Gone Girl’,” referring to the hit Ben Affleck thriller and novel “Gone Girl,” in which a small-town wife stages her own murder to get back at her cheating husband. 

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Vallejo’s police department headquarters is seen in Vallejo, Calif. on Tuesday, July 14, 2015. (Paul Chinn/The San Francisco Chronicle via Getty Images)

Although they said in a press conference that they were treating the case as a kidnapping, KRON4 reported, the Vallejo Police Department suspected Quinn of murdering his girlfriend and fabricating his account. He endured 18 hours of questioning, according to the docuseries. 

The couple sued the Vallejo Police Department for $2.5 million, but not before enduring months of public scrutiny.

Huskins and Quinn told filmmakers Misty Carausu, a rookie detective who solved the case, was their hero. On June 5, 2015, a couple woke in the middle of the night to a near-identical home invasion. 

After reaching out to police departments in the Bay Area, NBC Bay Area reported, Carausu learned that Muller had been a suspect in a 2009 Palo Alto home invasion. Also at the scene were a pair of swimming goggles blacked out with duct tape that had a blonde hair attached. 

While the wife hid in a bathroom and called police, her husband managed to fight off the attacker. But he left crucial evidence behind: zip-ties, duct tape, a glove and a cellphone. 

Carausu traced the phone to the stepfather of a man named Matthew Muller, a Harvard-educated immigration attorney and Marine veteran. 

At that point, Carausu contacted the FBI, and Muller was arrested for the Dublin, California, home invasion on June 8.

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Denise Huskins and Aaron Quinn are pictured at a press conference. They both hired defense attorneys after they were publicly accused of faking the home invasion, and feared losing their jobs as physical therapists.  (MIKE JORY/THE TIMES-HERALD via AP)

Evidence in his home, including Quinn’s laptop, finally linked him to Huskins’ kidnapping. Muller’s confession matched Quinn and Huskins’ stories perfectly, down to the audio recordings, blacked-out goggles and liquid sedatives. 

Muller pleaded guilty to one count of federal kidnapping in September 2016 and was sentenced to 40 years behind bars. Muller also faced state charges for burglary, robbery, kidnapping and two counts of rape by force.

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The Vallejo Police Department publicly accused Denise and Aaron of staging their ordeal, welcoming a barrage of negative press before their attacker was arrested for a similar home intrusion. (Associated Press)

But he was deemed incompetent to stand trial for those charges in November 2020, according to the documentary. Muller allegedly suffered from “Gulf War illness” after his military service, and his attorney claimed he was diagnosed with bipolar disorder, NBC News reported. 

Muller was then sentenced in 2022 to 31 years in state prison after pleading no contest to two counts of forcible rape of Huskins.

He is currently incarcerated in federal prison in Tucson, Arizona. 

Huskins and Quinn previously told People magazine they have no idea why Muller targeted them.

“Like many victims, or many people who have gone through tragedy, you don’t get all the answers,” Quinn told the magazine. “And that can be a sticking point to recovery. So, for us, we don’t rely on finding those answers, but what we have to do is move forward in the unknown and focus on things that matter the most to us, like our family, our kids, our work. Those are sustainable things. And having the answers of why they targeted us doesn’t change what we do as far as moving forward.”

The pair married in 2018, released a book on their ordeal in 2021 and welcomed daughters in 2020 and 2022.

Fox News Digital’s Christina Coulter and The Associated Press contributed to this report. 

Stepheny Price is writer for Fox News Digital and Fox Business. Story tips and ideas can be sent to stepheny.price@fox.com