Mangione, 26, is also charged with: two counts of second-degree murder, one of which is charged as killing as an act of terrorism; two counts of criminal possession of a weapon in the second degree; four counts of criminal possession of a weapon in the third degree; one count of criminal possession of a weapon in the fourth degree; and one count of criminal possession of a forged instrument in the second degree.
He's accused of gunning down Thompson outside a Midtown Manhattan hotel on Dec. 4 as the CEO headed to an investors conference.
"This type of premeditated, targeted gun violence cannot and will not be tolerated," Manhattan District Attorney Alvin Bragg said in a statement Tuesday.
The slaying in the heart of Midtown was "intended to cause shock and attention and intimidation," Bragg said at a news conference.
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In Pennsylvania, where Mangione remains in custody, he faces charges including allegedly possessing an untraceable ghost gun.
He is expected to waive extradition from Pennsylvania during his next court appearance on Thursday, sources said.
Mangione has hired Karen Friedman Agnifilo as his lawyer in New York. She was a 25-year veteran of the Manhattan District Attorney's Office and its second in command for eight years.
Mangione was arrested at a McDonald's in Altoona, Pennsylvania, on Dec. 9 after nearly one week on the run.
When Mangione was apprehended, he had a 9 mm handgun with a 3D-printed receiver, a homemade silencer, two ammunition magazines and live cartridges, prosecutors said
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Thompson's murder ignited online anger at the health insurance industry. Many people online have celebrated the suspect and some have donated to a defense fund for Mangione.
"Just a cold-blooded, horrible killing," President-elect Donald Trump said at a news conference Monday.
"It's really terrible that some people seem to admire him, like him," Trump said.
"It seems that there's a certain appetite for him. I don't get it," Trump added.
Sources said writings police seized from Mangione suggest he was fixated on UnitedHealthcare for months and gradually developed a plan to kill the CEO.
Among the writings recovered from Mangione was a passage that allegedly said, "What do you do? You whack the CEO at the annual parasitic bean-counter convention," according to law enforcement officials.
This is a developing story. Please check back for updates.