Shaak Ti and Vos form a plan to attack Shogar Tok's fortress which required Agen Kolar to launch a diversionary attack to the north. The attack was aimed to allow Shaak Ti and Quinlan Vos to infiltrate the fortress from the south and disable the shields and ion cannons, which would allow Master Koon to send his reinforcements. However, during the attack, Agen is captured and thrown jailed in the prison with his troops. Luckily, the plan worked and Masters Ti and Vos succeeded in infiltrating the fortress, destroying the shields and ion cannons, and killing Shogar Tok. During their escape, they freed Agen who rejoin Master Koon in orbit having won the Battle of Brentaal IV.
Later during the war, the Jedi feared that Jedi Master Quinlan Vos' mission to infiltrate Count Dooku's inner circle had him treading too close to the Dark Side. Agen Kolar tracked Quinlan Vos to Nar Shaadda where he attempted to arrest him. While Quinlan feigned submission to Agen's request, Vos maintained the persona that he was one of the dissident Jedi that felt the Jedi Council had erred in siding with the Republic. Master Kolar reaffirmed his stance that he believed the Council was correct. During transit back to Master Kolar's ship, Master Vos escaped Agen's custody and a chase ensued through the cityscape of Nar Shaadda. The two battled with lightsabers, but neither intended to hurt the other - Quinlan's only goal was escape with Agen's being apprehension.
The chase eventually led to a den of street thugs, gangs, and other unsavory types who were very offended that the Jedi Master was trying to arrest Vos, who they considered to be one of them. Agen Kolar had no problem fighting them to the last man, but the appearance of Aruk the Hutt forced Agen Kolar to consent defeat and return to Coruscant without Vos. Reporting in to the Jedi Council, Kolar was prepared to try to apprehend Vos again, but the Council informed him it was not necessary. Kolar also expressed his opinion that Vos had fallen to the Dark Side. The Jedi Council asked Vos to return to his troops in the field his mission with Vos complete.
In reality, the purpose of Master Kolar's mission was to solidify the belief that Master Vos had defected from the Jedi and fallen to the Dark Side in order to facilitate his infiltration into Count Dooku's inner circle. Vos was assigned to go deep undercover in an attempt to convince Count Dooku to allow him into his camp and set himself up as a spy. To make Vos' defection even more credible, a Jedi that was unaware of this mission needed to be convinced that Vos had actually defected in order to make Vos' position that much more credible. As one of the order's finest Jedi Masters, Agen Kolar fit that description perfectly.