A bulk of this episode was focused on Chloe and CTU's mission to stop Jack from exposing the Russian's terrorist attacks. This meant preventing him from getting to Dana Walsh, a job made more difficult when the President chose to move her to a secure location with a private security team. For what reason?
Because Logan convinced her this would help maintain the peace. They torture Dana, get the evidence about the Russians from her and then get rid of it. Case closed. Peace saved. Taylor goes for this ridiculous offer, causing Ethan to resign his post. Logan is quite pleased with himself as he watches Taylor introduce Dalia Hassan at the peace treaty press conference near the end of the episode, as viewers see a few shady dudes using physical coercion against Dana.
But back to Jack. He's on the lam in NYC and wants Chloe to tell him where Dana has been taken. Instead, she lies to him and sets up Cole and company at a safe house to apprehend Jack (who quickly gets a bunch of weapons from some dude in the city that owes him a favor). When Jack arrives at this location, supposely thinking it's where Dana is located, he takes down the CTU agents waiting for him. Without too much force, of course.
He tells Cole he figured out Chloe's plan, forces Cole to tie up his CTU pals and then tells Cole to join his plan. He says the President has lost it and wants to cover up the terrorist attack, and the two of them must stop this from happening. To do so, Jack must pretend to take Cole hostage, so CTU doesn't know they are working together, and the two must go find Dana and get the information about the Russians from her.
Cole agrees and that's what we find these two doing when the episode concludes.