Years after Hollingsworth was placed in charge of the Joes, the U.S. government chose a side in Cobra's civil war. In exchange for the return of a top secret "black box" stolen by Cobra, the Joe team entered the civil war on the side of Serpentor. The head of the Jugglers, General Malthus, authorized the deal, but funded the operation secretly (through a special services fund, recorded as payment for basketballs) and bought ammunition supplies from Destro's armaments corporation, MARS. The Joes came out on the losing side of the civil war thanks to a last minute deal among Cobra's high command. The Jugglers refused to take the fall for the failure and blamed Hawk and Hollingsworth, claiming they had entered the war with out any authorization from the Pentagon. Malthus -- who allied himself with U.S. Senator Hegel --  had Hawk and Hollingsworth arrested and placed in a Virginia hospital for psychiatric evaluation, safely away from the media. Nearly the entire Joe team was arrested as well, but a small group led by Roadblock eluded capture and stormed the hospital to rescue their commanders. A fire fight between the Joes and the hospital staff -- Domestic Operations Agency members working for Malthus -- and before the Generals were killed, Destro arrived via helicopter. In full view of the press, the weapons supplier gave Malthus the receipt for his purchase of ammunition. The Joes returned to action and Malthus spent the next few years in military prison at Fort Leavenworth. Hegel was spared any blame due to insufficient evidence. Later, he even tried to shut down the Joe team. (#77-78, 99)

Two years after the Cobra Island debacle, the Jugglers remained in place, now under the control of General Thurston Crowther. During a closed meeting of the committee, the generals were astounded by Storm Shadow's sudden entrance, crashing through the ceiling above their chambers. He had evaded security to force the Jugglers into giving Snake-Eyes a dangerous mission to break him out of his despair over Scarlett's comatose state. Having stolen the files on the highly classified and covered up "George Strawhacker case," Storm Shadow threatened to expose the fact that Strawhacker was allowed to rot in a Borovian prision for years. Strawhacker had been the fiancee of Snake-Eyes' twin sister before her death years before. But after Snake-Eyes left on the mission to rescue George, General Crowther captured Storm Shadow and Stalker, explaining that he learned the government didn't want Strawhacker rescued, since he had been leaking false information to the Soviets and his rescue would cast doubt on his traitorous behavior. Crowther sent in the former Cobra mercenary Major Bludd to kill Snake-Eyes so that no one would rescue George. After Snake-Eyes freed Strawhacker, the spy was killed by Borovian rebel leader, Metz. The former Soviet nation's new leader's were present when Bludd revealed his mission. Crowther continued to hound Snake-Eyes, Storm Shadow and Stalker until Hawk met with the General and told him that he should lay off the three Joes since the word of Borovia's head of state held more weight than Crowther's. (#103-108)

The Jugglers didn't cause any more trouble for the Joes for the years leading up to the team's shutdown in 1994. Some time later, Hawk himself became a member of the Jugglers, hoping to weed out the corruption from the inside. In 2001, the G.I. Joe team was reinstated under Hawk's command. He remained on the committee, vowing to shield the team from their political meddling and keep the Jugglers' power in check. So far, he has been successful. (v2 #1)