Operation Mentor was a fake task force set up by OPR Agent Garrett Fowler and a few of his colleagues in response to threats that Fowler received after he murdered the man who killed his wife. It was designed to entrap Neal Caffrey by using his girlfriend Kate Moreau to get him to steal an amber music box that had once belonged to Catherine the Great.
Kate was being held hostage by Fowler and they struck a deal, the deal being that Neal and Kate work for OPR as deep cover agents which would give them new identities and the chance to go anywhere.
Burke found out about the plan and realized that this was designed to let Neal disappear entirely as Fowler believed he was a let down to the FBI.
In order to disappear so effectively and in essence become an agent for OPR, Neal had to steal the Music Box which Alex had tracked down in the Italian Consulate. After giving him the box, Fowler gave Neal the paperwork for new identities and Kate's location. When getting to the airstrip where Kate and the plane was, the plane exploded with Kate inside.