On Jan. 27, law enforcement received information from a confidential source indicating that McWhorter, Morris and Hari were responsible for the bombing.
A fourth man Ellis Mack, 18, was arrested for possession of an assault rifle, federal prosecutors in IL said.
"That bombing that took place last summer has been a tragedy for all Minnesotans", said Greg Brooker, acting U.S. Attorney for the District of Minnesota.
"If you don't understand Muslims or Islam, then go and learn, be curious, inspire some empathy", said JaNae' Bates, pastor and ISAIAH communications director.
All four men are from Clarence, 35 miles (56 km) north of Champaign-Urbana.
A complaint said a tip in December led authorities to investigate the three men, after a person sent the local sheriff photos of guns and bomb-making material inside Hari's parents' home, where Hari often stayed.
McWhorter allegedly told an Federal Bureau of Investigation agent during an interview that the three rented a pickup in Champaign and drove more than 500 miles (805 kilometres) to Minnesota with a plan to bomb the mosque, according to a criminal complaint.
McWhorter, who said it was Hari's idea to bomb the mosque, said "they did not indent to kill anyone, but they wanted to "scare them out of the country" (referring to Muslims), because they push their beliefs on everyone else", the court document said.
According to the affidavit, Mr. McWhorter told a law enforcement official that during the attempted bombing at the Women's Heath Practice in Champaign, Ill., Mr. Morris had been dropped off at the clinic in the middle of the night, smashed the clinic window and thrown an explosive device inside.
The bomb was thrown into the imam's office. The pipe bomb exploded, causing a fire that was extinguished by sprinklers.
Anti-Muslim incidents rose sharply in the United States in the year after the 2016 US presidential election, according to a review by the Council on American-Islamic Relations.
"You can see it put a lot of cracks into the cement wall", center Executive Director Mohamed Omar said when the video was released.
The mosque primarily serves Somalis in the Minneapolis area. Minnesota has the largest Somali community in the United States, according to the most recent census estimates.
A video showed the explosion.
Gov. Mark Dayton called the bombing an act of terrorism when he and other officials visited the mosque the day after the explosion. There they found a pipe bomb attached to a propane tank, according to the affidavit.
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