Clarke — who was assigned to the IRS criminal investigations office in Boston at the time of the incident — was released on personal recognizance after a magistrate rejected a prosecution request that bail be set at $10,000 cash.

The allegations were made during the arraignment of James R. Clarke, 44, in Suffolk Superior Court. He pleaded not guilty to charges including aggravated rape, assault and battery with a dangerous weapon, and indecent assault and battery.

An Internal Revenue Service agent got a 21-year-old intern drunk last July and then allegedly handcuffed her in his government-issued car in Boston before shoving “his service weapon deep into her mouth” and raping her, a Suffolk prosecutor said Thursday.


Clarke and his father left court without speaking to reporters.

His lawyer, Michael Doolin, said during the brief hearing that his client and the young woman, who had an unpaid summer internship at the IRS, engaged in “consensual acts” on the night in question.

But Suffolk Assistant District Attorney Ian Polumbaum provided a starkly different version of the encounter, which began on the night of July 26 when Clarke invited the intern for drinks after work at the Kinsale pub at Center Plaza.

Clarke, Polumbaum said, bought the young woman “enough drinks to intoxicate her” before they walked to the agent’s vehicle in the Government Center garage. The woman had expected Clarke to drop her off at South Station so she could catch a train home, according to authorities.

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The government’s statement of the case said that when Clarke and the woman initially entered his car on the sixth floor of the garage, he handcuffed her “under the guise of showing her what it was like due to her interest in law enforcement work.”

He allegedly groped her upper body without consent and shoved his service weapon “deep into her mouth” before subjecting her to multiple sexual acts against her will, Polumbaum said.


According to prosecutors, Clarke then allegedly pulled the woman’s pants down and repeatedly raped her, telling her during the attack “that she liked pain.”

“The victim stated that she did not protest or resist due to fear from Clarke’s use of the handcuffs and the gun,” the statement said.

Clarke later drove the woman to South Station and allegedly grabbed her head, forcing her into another brief sex act, according to the statement.

“Asked if he ever touched the victim with the firearm, Clarke said it might have brushed against her face when he showed it to her,” the statement said. “Forensic testing, however, detected amylase (a main component of saliva) in a swab collected from the surfaces of the weapon; and at the time of her hospital exam the victim had a fresh injury to the uvula at the top of her throat.”

Once at South Station, the woman first called a friend to report the alleged assault and then called 911, according to prosecutors.

Polumbaum said Clarke told police the following day that the two had engaged in consensual sexual activity. The agent “specifically denied . . . doing anything with the firearm” and claimed it may have brushed up against her when he “let her look at it and handle it,” Polumbaum said.

That was contradicted by the forensic testing and medical records, he said. He also said the woman had injuries consistent with being handcuffed and grabbed by the neck.


Polumbaum asked that Clarke be held on $10,000 cash bail, noting that one of the charges he faces carries a mandatory 10-year prison term.

However, Assistant Clerk Magistrate Edward Curley agreed to release Clarke without bail, citing his compliance with the summons to appear for arraignment and the fact that “he’s made himself available to the Commonwealth for inquiry on the matter.”

Clarke was ordered to stay away from the woman and any civilian witness and remain in Massachusetts while the case is pending.

The graduate of Scituate High School and Suffolk Law listened stoically to the proceedings and stood in a dark suit with his hands folded in front of him.

Doolin, his lawyer, told reporters afterward that Clarke has “been completely cooperative” with police during the investigation.

“He’s an outstanding individual,” Doolin said. “He denies these allegations and he looks forward to litigating this case in a courtroom in front of a jury of his peers.”

Doolin declined to comment on Clarke’s duty status with the IRS. Polumbaum said during the arraignment that Clarke has “or at least had, until recently, a job as a federal agent.”

The Globe first reported on the assault allegations in November, noting that Clarke had not been arrested and was allowed to continue working at the IRS, despite the ongoing investigation.

The IRS declined to discuss his employment status after his indictment last month and said Thursday that the agency can’t discuss individual personnel matters.


“The IRS cannot comment on specifics involving these serious and disturbing allegations,” the agency said in a statement. “The IRS holds our employees to high standards, and we do not tolerate inappropriate behavior.”

After announcing the indictment against Clarke in March, Jake Wark, a spokesman for District Attorney Daniel F. Conley, said, “The joint investigation by Boston police and Suffolk prosecutors entailed multiple interviews, forensic testing, a review of medical records, and an exhaustive grand jury presentation to build the strongest case possible.”

Clarke’s next court date is slated for May 9 for a pretrial conference.

Shelley Murphy of the Globe Staff contributed to this report. Travis Andersen can be reached at tandersen@globe.com.