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After opening with Chuck shooting a person, we travel back three days to find out that Chuck is about to embark on his final exam to become a full-fledged spy. Chuck is going it alone, getting direct orders from Beckman, and only having Sarah along for notetaking. Chuck is sent to spy on ring operative named Anatoly (aka Ivan Drago) at a spa and find out who the CIA mole he's working with is. Chuck has a stakeout with Sarah to identify Anatoly but ends up getting distracted by discussing feelings with Sarah. After they're about to kiss, Shaw calls to let them know Anatoly is in the building. Chuck heads in and after a steam room scene with some gratuitous shirtless Zachary Levi, Chuck gets a good look at the mole, Hunter Perry. Chuck believes he completed his mission and has become a spy.
Meanwhile, Casey is still trying to adjust to civilian life and with no other plans, is still spending his time at the Buy More. After knocking out Jeffster, Big Mike tries to calm Casey down with some new feathers and makes him apologize to Jeffster over some Subway sandwiches. Chuck gives the newly calmed Casey a government-issued gun as a way of saying thank you for helping him become a spy.
Sarah asks Chuck to dinner where she reveals the last part of the mission: to kill Hunter. Hunter shows up to where they're having dinner and sits down with Chuck, believing him to give him CIA info. Hunter obviously catches on and bolts to the bathroom where Chuck follows him. Chuck can't bring himself to kill a begging Hunter and says he'll arrest him instead. While walking him out of the bathroom, Hunter makes a run for it, and Chuck chases him down. Again, Chuck has a gun pointed at Hunter and is unable to pull the trigger. When Hunter starts to pull a gun, Casey pops out of the shadows and kills the baddie. Even as a civillian.
At the end, Chuck gets credit for killing Hunter and becomes a spy. He tries to call Sarah, who we cut to ignoring the phone call and saying she no longer loves Chuck now that he becomes a killer. In the end a woman comes to pick up Chuck to take him to Washington.