BOSTON (CBS) — A former MBTA Transit Police officer was held on $1,000 bail for allegedly beating a Roxbury woman at the Dudley Square T station two years ago after that woman spoke out about possible abuse by the officer.

Jennifer Garvey, 33, walked into Suffolk Superior Court Wednesday on her own free will and pleaded not guilty to charges of causing injury while violating a person’s civil rights, assault and battery with a dangerous weapon, assault and battery, and two counts of filing a false report.

Prosecutors say Garvey used excessive force against bystander Mary Holmes, a Roxbury woman who said she was attempting to de-escalate a disturbance between police and an elderly woman at Dudley Square on March 26, 2014, and then filed false reports about the incident.

Prosecutor: Jennifer Garvey repeatedly struck the bystander–Mary Holmes–with her police baton, then filed false reports about incident. — Carl Stevens (@carlwbz) January 13, 2016

Holmes said Garvey and officer Alfred Trinh screamed at and shoved the woman, whom she recognized as a fellow commuter she had interacted with before. The woman was being arrested for public intoxication. Prosecutors said Holmes initially urged the woman to comply with police, but became worried that Garvey was being too forceful.

Holmes can be seen in MBTA surveillance video calling 911 to report Garvey’s behavior. Prosecutors say that’s when Garvey pepper-sprayed her and beat her with a baton, before arresting her for assault and battery on police officers.

Prosecutor: witnesses did not see anything that justified former #MBTA Officer Garvey's use of pepper spray against Mary Holmes. — Carl Stevens (@carlwbz) January 13, 2016

Holmes suffered burning eyes from the pepper spray, an open wound on her shin that required stitches, and bruising to her legs and ankles. She was arraigned on charges the next day–but now the situation is reversed, with Garvey facing charges and Holmes cleared, and the American Civil Liberties Union calling this case a rare and important victory for human rights.

“This is 180 degree shift from what happened,” said Carl Williams, staff attorney for the ACLU. “Today, a little piece of justice has been brought because Mary Holmes stood up that day for members of her community.”

The case took two years to come to court. Williams acknowledged that it “took a little bit of time,” but said the ACLU applauded the action because they appreciate how rare these cases are.

Garvey’s defense argued that the incident was a civil, rather than criminal, matter. They noted that the MBTA initially cleared Garvey of any inappropriate use of force, and said she sought mental health treatment on her own for PTSD that resulted from her military service. She was honorably discharged from the military after two tours in Afghanistan.

“She plans on aggressively defending this case,” Defense attorney Douglas Louison said. “I anticipate once the facts come out, she’ll be acquitted. It was an appropriate use of force during a difficult situation that police officers often find themselves in … unfortunately many uses of force often look jarring and look violent.”

The MBTA Transit Police Department terminated Garvey’s employment a few weeks ago.

Holmes, who was present in court for Garvey’s arraignment Wednesday, sued the MBTA last summer for police brutality and violating her civil rights.

In addition to posting bail, Garvey is required to be alcohol free, check in with a probation officer weekly, and continue mental health treatment for her PTSD. She will be back in court February 9.

WBZ NewsRadio 1030’s Carl Stevens reports