The Pennsylvania Office of Attorney General filed the charges against 37-year-old Kendall Stephens.
Philadelphia Police Special Victims Unit received reports of sexual assaults on two minor children in September 2023.
Stephens is charged with two counts of Rape, Indecent Assault, Endangering the Welfare of a Child, Corruption of Minors, and other related crimes.
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A judge set her bail at $250,000 and her next court appearance is scheduled for December 29.
The AG's office often takes on cases from local district attorneys if they have a conflict in the case.
In a statement to Action News, a spokesperson for the Philadelphia District Attorney's Office says, "The investigation of allegations against her is being led by another agency, and as such we have no comment."
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The prominent LGBTQ+ activist came to Action News in August of 2020 after she was attacked in her Point Breeze neighborhood. She says she was targeted by a violent group for being a trans woman.
Stephens then became a prominent activist for the LGBTQ+ community and she urged lawmakers to change Pennsylvania's hate crimes statute to include protections for LGBTQ+ people.
Action News was there for a 2021 press conference where Stephens, along with several other activists, stood by District Attorney Larry Krasner to help launch the LGBTQ+ Advisory Board.
The board was created in part to be a source of information and resources for victims and survivors of crime, within the community.