Boston Internal Revenue Service employee is accused of shoving his gun in an intern's mouth before raping her in his car, according to court documents.

James Clarke was arraigned Thursday on charges related to an evening last July he spent with a female intern at the Boston IRS office.

According to Suffolk County District Attorney Dan Conley, Clarke was having drinks with the intern before he offered to drive her back to South Station so she could catch a train.

It was inside Clarke’s IRS-issued car on the sixth floor of the Government Center parking garage where he allegedly handcuffed her under the guise that she was interested in police work.

However, the district attorney’s office said that’s where Clarke took the interaction too far.

Court documents state Clarke left the woman handcuffed and shoved his gun into her mouth, which the DA said is supported by a fresh injury to the woman's uvula found later that night at the hospital.

The documents state he groped her upper body and digitally raped her, telling her, “she liked the pain.”

Clark drove the woman to the train station where, while parked on a street, he allegedly forced her head down and put his penis in her mouth before letting her out of the car.

The woman called a friend and then 911. She was taken to the hospital.

Police said Clarke confirmed the basic details of the evening the next day but said the woman was a willing participant. He also said his gun might have brushed her face, but forensic investigators found saliva along the surfaces of the weapon.

In a statement sent, the IRS said it “cannot comment on specifics involving these serious and disturbing allegations.”