Burke took over as Director of Field Operations after Cole Ortiz was arrested for assisting Jack Bauer. Just before leaving CTU for the UN building, Chloe informed Burke that Cole would be coming with them. Burke was displeased with the idea, thinking him a traitor working against CTU. Chloe dismissed his fears. Later, when at the Mobile Command Unit, Chloe told Burke that Cole would be taking over as Director of Field Operations again. He gave Cole a weapon and badge, and said that the updated security protocols were ready.
After Chloe had shot Jack Bauer, she tried to leave and return to the Mobile Command Unit to pass off Jack's recording. However, on Jason Pillar's orders Burke stopped her so that Pillar could search her, fearing that she was working with Jack. Pillar was unable to find the chip and so he let her go. When she returned and began to upload the chip to the CTU servers for Arlo Glass to distribute, Burke once again tried to stop her. Cole tried to defend her but Burke and another agent overpowered him and they took Chloe and Cole into custody.