Four people were injured in the crash, including the trolley operator.
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Brianna Satchell-Thomas, 31, is facing several charges, including aggravated assault while DUI, simple assault, recklessly endangering another person and failure to stop at red light.
The crash happened around 6:25 a.m. Sunday on the 1300 block of South 52nd Street.
SEPTA officials tell Action News the driver of the car crashed into the trolley after running a red light, knocking the trolley off the tracks.
According to the Philadelphia district attorney's office, police arrived on the scene to find a white Mercedes with major damage.
Witnesses told police the occupants of the Mercedes fled the scene.
However, the D.A.'s office says Satchell-Thomas later returned. She was allegedly trying to recover belongings from the Mercedes, which investigators say was registered to her.
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She was then placed under arrest.
"Defendant Satchell-Thomas is alleged to have driven while under the influence and in such a reckless manner to have caused the crash involving the trolley, which was carrying passengers at the time," the D.A.'s office said in a news release.
SEPTA said Satchell-Thomas is a maintenance custodian but was not working, or on her way to or from work, at the time of the crash.
SEPTA went on to say there was nothing the trolley operator could do to avoid the collision.
The D.A.'s office said that since the crash involves a SEPTA employee and a SEPTA vehicle, the case will be prosecuted by its Special Investigations Unit.
According to the D.A.'s website, the unit is a "team of prosecutors, investigators and support staff pursue active prosecutions against government officials, public servants and members of law enforcement who are accused of misconduct."