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Victor Pena, the man accused of abducting a 23-year-old woman in downtown Boston and holding her captive for three days in his Charlestown apartment, will continue to be held without bail after he was charged with three counts of aggravated rape.

Pena, who appeared in shackles on his wrists and ankles Friday at Charlestown Municipal Court, previously had been arraigned Jan. 23 on charges of kidnapping the woman after she left a bar near Faneuil Hall. Pena was seen on video following her as she walked down Congress Street, officials said.

Police conducted a citywide search and found the woman inside Pena’s apartment in the Bunker Hill housing development, where Pena had installed extra locks on the front door, according to court documents.

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The Globe does not identify alleged victims of sexual assault without their consent. After she went missing, authorities had named the woman in an effort to find her.

Judge Lawrence McCormick ordered the rape charges impounded, but court records confirmed the allegations. Pena, 38, is scheduled to be arraigned March 15 on the new charges and undergo a dangerousness hearing to determine whether bail will be allowed.

Pena has been deemed competent to stand trial after a psychiatric evaluation at Bridgewater State Hospital, according to his lawyer, William Barabino.

Barabino said there had been “no issue until the police came” and said Pena voluntarily opened the door when police began drilling into locks to his apartment. Authorities have said that Pena seized the woman’s cellphone, but Barabino said the woman was on a phone under her control when police arrived.

Authorities have said she was sobbing and horrified when they rushed into the apartment and subdued Pena.

“We’re adjusting as we take in the new information,” Barabino said of the rape charges. “It’s a fluid situation.”

After the woman left Hennessy’s bar late on the night of Jan. 19, surveillance video showed Pena following her, putting his arm around her waist, and apparently guiding her toward the MBTA’s State Street Station, police said.

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When the woman did not answer phone calls the next day, her twin sister used a tracking app to locate her phone at Walford Way and Corey Street in Charlestown, the location of the apartment building where Pena lived.

Despite an intense search, another two days would pass before police found the woman at Pena’s apartment.

Jose Pena, the defendant’s older brother, said at the courthouse that his brother is innocent.

“He’s definitely not a criminal,” said Jose Pena, who cut short a vacation in Puerto Rico to attend the court session. “Eventually, the truth will come out.”

Jose Pena said that his brother has the mental capacity of a 13-year-old and is not competent to stand trial.

At least one former girlfriend has accused Victor Pena of sexual assault, according to court documents connected with a 2004 restraining order issued in Dorchester.

“He has hit me, he has forced me to have sex, and he has insulted me constantly,” the former girlfriend wrote in her application for the order. “My children are scared of him, especially the younger one, and I’m afraid he might hurt me or the children.”

At that time, according to court records, Pena was staying at the Lemuel Shattuck Hospital Shelter for Homeless Men in Jamaica Plain.

In 2008, another woman, who had a child with Pena, took out a restraining order against him because she feared for herself and her 2-year-old daughter, according to the application.

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A third woman wrote in a 2013 restraining-order application that when she ended a two-month relationship with Pena, he punched her and began calling and messaging her with explicit and humiliating sexual taunts.


Brian MacQuarrie can be reached at brian.macquarrie@globe.com.