Police arrested Johnathan Lincoln near the Berkeley Police Department last week (file photo). Photo: Kaia Diringer

It’s the nightmare scenario that rarely happens: A stranger with a knife raped a young woman working alone late at night in a downtown Berkeley shop last week, authorities report.

The attack, which was recorded on surveillance video, was interrupted when another customer went into the business. Police say they caught the rapist several blocks away, and that he was identified by three witnesses and the victim as the person responsible for the crime.

Most sexual assaults happen in much more mundane circumstances. It’s usually someone you know. Very rarely is the attacker an armed stranger who strikes out of nowhere. According to the Alameda County Family Justice Center, “About 75% of rapes are committed by someone the victim knows.”

But that wasn’t the case here. Last Wednesday night, shortly before closing time, a woman was working alone in a downtown Berkeley business and getting ready to shut down for the night. (Berkeleyside is not including further location information so as to shield the identity of the victim, whose name has been suppressed from court papers due to the nature of the crime.)

According to court documents, the man walked inside the business sometime before 10:45 p.m. and forced the woman into the back storage room, where he raped her and forced her to perform oral sex. He “did this while holding a knife to the victim’s neck” and threatening to “slit your throat,” police said.

When another customer walked inside, the rapist broke off the assault, grabbed $430 from a desk where it had been set to be counted, and fled the scene, according to court papers.

Police detained the man several blocks away, in the 2100 block of Martin Luther King Jr. Way across from the Berkeley Police Department, just before 11 p.m.

The woman was taken to the hospital with non-life-threatening injuries.

Officers took the man, identified as Johnathan Lincoln, to Santa Rita Jail. Authorities said he tried to take seven ecstasy pills into jail with him, which is illegal.

According to court papers, Lincoln was on felony probation for burglary and has prior arrests for sexual assaults.

Lincoln, who is 29, has no listed home address in court documents but is from Oakland, police said.

He has been charged with forcible rape, including special allegations for the use of a knife and kidnapping; forcible oral copulation, with the same special allegations; and second-degree robbery, also with a special allegation for the knife. Special allegations can increase the severity of sentencing.

Lincoln could be sent to prison if he is found guilty.

He has three prior convictions, for grand theft from a person in San Francisco in 2007, for burglary in Alameda County in 2013, and for burglary in San Mateo County in 2014. Two of those convictions, including the San Mateo County case, sent him to prison. He has one strike, and the current case would also count as a strike if Lincoln is convicted, according to court documents.

He also faces a special allegation for being on probation at the time of his arrest last week.

Lincoln is being held without bail at Santa Rita Jail and is scheduled to enter a plea Feb. 14.

According to online records from the Alameda County sheriff’s office, Lincoln also was arrested over the weekend, while in custody at Santa Rita — just before 2 a.m. Saturday — on suspicion of assault with a deadly weapon causing great bodily injury.

Police ask anyone with information about the Berkeley case to call BPD’s Special Victims Unit at 510-981-5735.

Bay Area Women Against Rape, or BAWAR, offers a 24-hour crisis line at 510-845-7273. BAWAR provides free in-person counseling to survivors of sexual assault and their significant others, and offers support groups, community education and other resources. The Sexual Assault Response Team at Highland Hospital can be reached at 510-534-9290 or 510-534-9291. Find additional resources online for survivors of sexual violence.

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Emilie Raguso (former senior editor, news) joined Berkeleyside in 2012 and covered politics, public safety and development until her departure in 2022. In 2017, Emilie was named Journalist of the Year...