The Mission to Nar Shaddaa was an opportunity for Quinlan Vos, who had been working undercover gathering intelligence for the Jedi Council, to appear as if he was no longer a part of the Jedi Order. By doing this, Vos would be able to infiltrate deeper into the Separatist's inner circle.
Following reports that linked Vos to the events that took place on Brentaal IV, many Jedi started to think he might have really been a traitor. However, the Jedi Council kept their faith in him and allowed him to "defect" from the Order. They sent an unknowing Agen Kolar to go after Vos on Nar Shaddaa.
On the Smugglers' Moon, Kolar encountered Vos and the two dueled. Kolar, believing that he was doing his duty to punish the traitor, nearly killed him, but Vos escaped, just as planned. The Jedi Council now had their operative deeper in the enemy's ranks.