Surveillance video shows the suspect walk into the co-cathedral of St. Joseph in Prospect Heights.
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Police said he approached a nun who was praying in a pew, and threatened her.
When the nun looked at another woman in a nearby pew, the man allegedly told her, "She can't help you, I'm going to kill you."
That's when the nun ran and called police.
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No one was hurt during the bizarre confrontation.
Police are investigating the case as a possible hate crime.
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