Six others also arrested Wednesday in the raid of the South Side apartment where they were staying were released Friday without charges being filed.
One of those protesters, Occupy activist Darrin Annussek of Philadelphia, denied there were Molotov cocktails in the apartment or that raw materials had been compiled.
"No way," Annussek said. "If I had seen anything that even resembled [a Molotov cocktail], I would have left."
He said that during 18 hours in custody, police never told him why he was arrested, read him his rights, or allowed him to make a phone call. He said he remained handcuffed to a bench, even after asking to use a restroom.
On the eve of the summit, the dramatic allegations were reminiscent of previous police actions ahead of major political events, when officials moved quickly to prevent suspected plots but sometimes quietly dropped the charges later.
Prosecutors said the three men were self-described anarchists and told a crowded courtroom that they intended to create mayhem in Chicago. A state's attorney cited one of three men boasting weeks earlier about the damage they would do in Chicago.
"After NATO, the city will never be the same," he quoted the man as saying.
At one point, one of the men asked the others if they had ever seen a "cop on fire."
Police Superintendent Garry McCarthy dismissed the idea there was anything more to the arrests than police responding to "an imminent threat."
"When someone was in the position [of having] Molotov cocktails - that's pretty imminent," he said. "It was not a completed investigation."
The suspects are Brian Church, 20, of Fort Lauderdale, Fla.; Jared Chase, 24, of Keene, N.H.; and Brent Vincent Betterly, 24, of Oakland Park, Fla.
If convicted on all counts - conspiracy to commit terrorism, material support for terrorism, and possession of explosives - the men could receive up to 85 years in prison.
Most Chicago neighborhoods were quiet Saturday, but scattered groups of protesters gathered in parts of the city.