The publication of that cartoon brought angry protests from Muslims around the world.
The FBI had been tracking the activities of the two men for some time, monitoring their phone conversations, their Internet activities as well as overseas trips taken by one of the men, David Coleman Headley.
Investigators say one of those trips took Headley to Pakistan where he met with an al Qaida-linked terrorist leader. The purpose was to recruit and ultimately carry out terrorist attacks in Denmark.
Four years ago, there were widespread protests throughout the Muslim world after a Danish newspaper published cartoons showing satirical depictions of the Prophet Mohammed. The protests, some of which resulted in deaths, continued for months, with some protestors demanding that the cartoonist pay with his life.
Federal prosecutors say that was the aim of two Chicago men, Headley and Tahawwur Rana, who were allegedly orchestrating terrorist attacks in Denmark with the specific intent of killing the cartoonist. Investigators say they referred to their plan as "the Mickey Mouse Project".
A year ago, Headley, whose given name is Daood Gilani, expressed his disdain for the cartoons on an Internet discussion site saying, "call me old-fashioned, but I feel disposed towards violence for the offending parties."
The FBI says Headley conducted extensive surveillance in at least two trips to Copenhagen this year, and posing as a businessman, even visited the newspaper offices he was allegedly targeting. He was headed back there earlier this month when agents arrested him at O'Hare with Copenhagen street maps and detailed video recordings.
Investigators say Rana, who lives on the North Side of Chicago, arranged for Headley's travels, both to Copenhagen and Pakistan, where he allegedly met with high-ranking terrorist leaders.
Rana owns a company called First World Management that includes the Immigrant Law Center on Devon. It's been closed since being raided by agents earlier this month.
Agents also raided a meat-processing operation and farm owned by Rana, located in the small town of Kinsman 50 miles southwest of Chicago.
Both Rana and Headley are in custody in the Metropolitan Correctional Center.
Rana is due in federal court Wednesday for a detention hearing.
His attorney says that Rana is a well-respected businessman who adamantly denies the charges and eagerly awaits the chance to contest them in court.