35-year-old Angel Uriarte has been charged with assault on a federal officer involving a weapon, discharging a firearm in relation to a crime and being a felon in possession of a firearm.
ATF agents say Uriarte opened fire during a standoff, which ended with his arrest.
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Agents returned fire, hitting Uriarte and hospitalizing him.
He recovered and pleaded not guilty to the Goshen killings, along with Noah Beard, the second suspect connected to the murders.
Both are due back in court next month.