After the mission to Nar Shaadda, Agen Kolar joined Jedi Masters Mace Windu, Kit Fisto, and Saesee Tiin on a mission to deal with the Crimson Nova chapter of the Bounty Hunters Guild, which had begun accepting bounties on Jedi at the request of Kh'aris Fenn at the orders of Count Dooku. The Crimson Nova operated out of the Rig, a space station located in the Stenness Node. The mission had Agen Kolar and Kit Fisto arrive at the Rig as capture prisoners. Saesee Tiin arrived disguised as a trader, and Mace Windu arrived in the open. With everyone in place, Agen Kolar and Kit Fisto escape from their prison cell and incite a prison riot. The distraction allowed the Jedi to launch their attack against the bounty hunters and attempt to discover who ordered the bounties.

During the fighting, the havoc created by the Jedi prevented the bounty hunters from reinforcing each other allowing the Jedi to confront Mika, the leader of the Crimson Nova. Mika wished to fight the Jedi to the death, but her second-in-command, Stroth, was smarter and stunned her before she could get herself killed by the Jedi. Stroth had not wanted to take the bounties on the Jedi and agreed to cancel the contracts. He also provided them with information on where to find Fenn, who kept his base on Ryloth. Traveling to Ryloth to confront Fenn, Agen and the Jedi arrived to find him dead. He was killed by Quinlan Vos under orders from Count Dooku who feared Fenn's failure would leave a trail back to Dooku. A holorecording left by Quin led Jedi Masters Fisto, Tiin, and Kolar to believe Vos truly had fallen to the Dark Side. All but Master Windu were unaware of Vos' undercover mission for Dooku.

Agen Kolar's service in the Clone Wars would also see him fighting alongside Jedi Knights Aayla Secura, Voolvif Monn, and Anakin Skywalker as they battled Separatist forces. At the end of the war, Agen Kolar was stationed on Coruscant when the Separatist launched their invasion attack against Coruscant and kidnapped Chancellor Palpatine. During the Battle of Coruscant, Agen Kolar piloted a Jedi Interceptor as he battled the Separatist fleet.

The battle would see the death of Count Dooku and was the beginning of the end of the Clone Wars. It also signaled the final step necessary for the Sith to exact their revenge against the Jedi. Not long after the battle, it was revealed that Chancellor Palpatine was the Sith Lord that had eluded the Jedi during the course of the war. Upon learning this, Jedi Master Mace Windu put together a strike team to arrest Palpatine. Master Windu chose Jedi Masters Saesee Tiin, Kit Fisto, and Agen Kolar to join him in the confrontation with the Sith Lord.