SAN JOSE — When the woman said she didn’t want to stay home after arguing with her husband, the cop took her to a hotel.

He waited in the parking lot until a second officer left on another call. Then, according to an allegation that has shaken the San Jose Police Department and public trust, patrolman Geoffrey Graves returned to the room, where he shed parts of his uniform but left on his bulletproof vest — and raped her.

The astonishing accusation spurred a five-month investigation into the September incident that led to the arrest Monday of Graves, 38, a Gilroy resident and six-year member of the police force.

Graves turned himself in to police and was booked into the Santa Clara County Jail on suspicion of one count of forcible rape. He spent no time in custody, quickly posting the required $100,000 bail. His arraignment is set for March 24.

Requests for comment were not returned by Graves, who before joining SJPD served with the Shasta Lake Fire Protection District from 2002 to 2004. It was not immediately clear whether he has hired an attorney.

SJPD’s preparation for the fallout was evidenced by a department statement — sent out first thing Tuesday after city officials, including City Council members, were notified the previous evening — that immediately sought to portray Graves’ suspected misconduct as an isolated case.

“This is an extremely serious allegation, and if proven true, the officer will be held accountable,” police Chief Larry Esquivel said in the statement. “While this incident is very troubling and tugs at our integrity, it is an isolated incident and by no means a reflection of our officers who perform their duties with honor and professionalism on a daily basis.”

Graves’ arrest is easily the biggest public-relations challenge for Esquivel since he became the permanent chief in December after serving as the interim chief for most of 2013.

“There are certainly a lot of people in the community who are watching to see what the new chief will do in different situations,” said Richard Konda, executive director of the Asian Law Alliance. “People are watching how he handles this.”

The beleaguered police department already has been dealing with an exodus of officers, amid an acrimonious fight with the police union over wages and benefits, as well as rising crime figures.

“San Jose is still a pretty safe city,” said Kyle Graham, a Santa Clara University School of Law assistant professor and former deputy district attorney. “But there is no way to spin this. It’s not good news for the police department.”

LaDoris Cordell, a retired judge who serves as the city’s Independent Police Auditor, said that alongside the criminal charge, a complaint about the incident was filed with the police department’s Internal Affairs division, which in turn is monitored by her office.

Any administrative or disciplinary actions against the officer would not occur until the conclusion of the criminal case. If Graves isn’t convicted, he could still be eligible for department discipline, which relies on a “preponderance of evidence” of misconduct rather than the more stringent “beyond a reasonable doubt” standard required in criminal court.

“It’s very sad and disturbing,” Cordell said of the rape allegation.

Graves was one of four San Jose police officers who shortly after 2 a.m. Sept. 22 responded to a report of a family disturbance at the San Jose home of the victim and her husband. The officers noted that the couple had been drinking, but did not find evidence of a crime.

The woman, a hotel maid, told officers she wanted to stay for the night at a nearby hotel where she once worked. At 2:32 a.m., Graves drove her to the hotel. Police say a second officer in another patrol car followed them.

About 20 minutes later, the second officer told dispatchers he was leaving to respond to another call. Graves’ patrol car remained in the parking lot for about 40 more minutes, according to a statement of probable cause written and signed by Sgt. Craig Storlie of the SJPD Internal Affairs Unit and Criminal Investigation Detail.

About 15 minutes after the second officer left, the woman was awakened by knocking on her room door. It was Graves, Storlie wrote. The officer entered the room, grabbed the woman, and pushed her onto the bed.

“The defendant took off parts of his uniform with the exception of his bullet proof vest,” partially undressed the woman, and climbed on top of her as she “resisted with verbal and physical communication,” Storlie wrote.

The report goes on to say Graves “forcibly engaged in sexual intercourse with the victim before leaving the hotel approximately 10 minutes later.”

Carlos Vega, the deputy district attorney prosecuting Graves, said the attack was first reported to the California Highway Patrol, which then notified SJPD. Storlie’s report said that occurred Oct. 13, three weeks after the alleged attack.

The department launched an investigation, and Graves was placed on paid administrative leave Oct. 17.

“Physical evidence corroborates the victim’s allegations. The victim positively identified the defendant during the investigation of this incident,” Storlie wrote.

After five months, police, in cooperation with the district attorney’s office, obtained an arrest warrant for Graves.

Graham said most police cases involve allegations of excessive force or manipulation of evidence.

“But this is an officer allegedly committing a serious felony that just came out of the blue,” Graham said. “You’re left asking: What officer would do this? That’s exactly what a good defense attorney will ask at trial.”

Contact Robert Salonga at 408-920-5002. Follow him at Twitter.com/robertsalonga.