Finch calls Reese while leaving his job at IFT in episode 1x02 "Ghosts".
Reese and Shaw track a Decima agent to a rooftop, but he jumps off before they can question him in episode 3x22 "A House Divided".
Harold is taken to an empty office building where he has a chat with Greer in episode 3x21 "Beta". Greer chats with Harold about the future and their Machines in episode 3x22 "A House Divided". Shaw, Reese, and Hersh watch the beginning of the trail broadcast and then fight off several Decima agents in episode 3x23 "Deus Ex Machina".