As the World Trade Center case unfolded, investigators uncovered a second, potentially far more deadly plot-a threat posed by a radical Islamic terrorist group. It soon becaine apparent that this group planned to strike out against the United States, and intended to commit these acts in the New York City area. Investigation by the JTTF revealed that these individuals were making explosive devices and intended to use them on such targets as the Lincoln and Holland tunnels, the United Nations headquarters building, and the federal building that houses the FBI New York Field Office.

On June 23, 1993, JTTF members raided the group's safe house and found its members making bombs they planned to use during simultaneous attacks on the four targets. As a result of this investigation, the JTTF made 15 arrests between June 24 and August 23, 1993. The arrests prevented the group from carrying out acts of planned terrorism, including murders and bombings. The arrests also increased confidence in the ability of law enforcement, working in concert on the federal, state, and local level, to protect the lives and businesses of the residents of New York City.

Five of the 15 defendants pleaded guilty or became government witnesses. Ten of the defendants went on trial in federal court on January 9, 1995. On October 1 of that year, a jury found all 10 defendants guilty of a total of 25 criminal charges. On January 17, 1996, the defendants received sentences ranging from 35 years to life plus 65 years.