During the Separatist Crisis the senate began to debate the Military Creation Act, which would create an army for the Republic for the first time in a millennium. During the debate, Senator Farr became a strong Militarist and supporter of the Act. He was known as a watchdog against Separatist influences in the senate and was highly critical of Supreme Chancellor Palpatine's Loyalist Committee, going so far as to claim it was a shadow government. After exposing Senator Havriso Looruya's Separatist ties, Farr was granted a position on the Loyalist Committee, an appointment that confused many members of the Senate. Despite the appointment, he continued to be critical of the Chancellor's handling of the Separatist Crisis, claiming that Palpatine was following his own agenda to the detriment of the Republic.
In 22 BBY, the Separatist Crisis exploded into the Clone Wars, a galaxy-wide conflict between the Republic and the Confederacy of Independent Systems. Emergency Powers granted to Palpatine resulted in the creation of the Grand Army of the Republic without the Military Creation Act ever coming to a vote. Farr was installed as the head of the Senate Action Subcommittee for Corellian Trade Spine Defense, a position he used for personal advancement. Around the beginning of the war, supplies en route to Farr's homeworld of Rodia became the repeated targets of pirates. After Rodia's pleas for assistance were consistently ignored by the Republic, Farr abandoned the Senate and joined the Confederacy of Independent Systems. In exchange for much-needed supplies, Separatist Council member Nute Gunray demanded that Farr aid him in capturing the Rodian's long-time friend, Senator Padme Amidala of Naboo. Amidala came to Rodia in order to aid in the supply crisis, but was instead imprisoned by Farr and Gunray's Battle Droid forces. After learning Gunray's plan to execute Amidala, Farr realized the error in his decision to join the Confederacy and turned on the Separatist leader. Farr then assisted Amidala and Representative Jar Jar Binks in arresting Gunray and turning him over to Republic forces.