Brian Church, Jared Chase and Brent Betterly were charged in Cook County Circuit Court with conspiracy to commit terrorism, material support for terrorism and possession of an explosive or incendiary device.
The charges come as Obama and dozens of other world leaders are arriving in Chicago for the two-day North Atlantic Treaty Organization summit to discuss global issues. The city has been filled with protesters demonstrating about wars, immigration and other concerns.
Lawyers for the men said earlier the arrests were merely a way for authorities to harass legitimate protesters with trumped up charges. They said investigators only found home beer brewing equipment when they raided the apartment on the city's south side earlier in the week.
Prosecutors, however, painted a different picture in the charging documents. They wrote that the trio made Molotov cocktails out of empty beer bottles, gasoline and cut up bandanas. The records indicate investigators found four such firebombs in the apartment along with plans for making pipe bombs. The items were discovered after Chicago police, along with the FBI and U.S. Secret Service, obtained a no-knock search warrant to raid the place.
Prosecutors also revealed that investigators apparently had an informant or undercover agent inside the group who reported back on their activities. One of the defendants, according to the documents, said at some point: "After NATO, the city will never be the same" and Chicago "doesn't know what it's in for."
Additionally, the records allege the trio managed to amass an unusual collection of weapons, including swords, throwing stars and a hunting bow, which they planned to use during their operations.
Beyond the Obama campaign headquarters and mayor's house, the trio allegedly also talked about firebombing Chicago police headquarters and numerous police stations to slow the emergency response to their other activities.
Michael Deutsch, a lawyer for the defendants denied that they were anything but peaceful protestors and called the arrests "entrapment to the highest degree," according to the Tribune. "What we believe is that this is a way to stir up prejudice against people exercising their First Amendment rights."