The NYPD says 56-year-old Derrick Gadson of Brooklyn is facing hate crime and drug charges.
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Surveillance video showed a shirtless man walking into the Co-Cathedral of St. Joseph in Prospect Heights Wednesday afternoon.
He approached Sister Maria Amador as she was praying in a pew and threatened to kill her.
Sister Amador said the man told her, "I don't believe in this because you don't help the poor".
When she looked over to a woman sitting nearby, the man said, "She can't help you. I'm going to kill you."
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The nun ran out of the way, calling for help.
"Now I'm safe, I'm fine, but when I watch the video again and I realize that was real, the story could be another way, it could be a hate crime," said Sister Amador.
The man left when the church organist stepped in to help.