Many viewers are confused by Sarah’s apparent behavior in the first episodes of season 3. The most common objection is about her rejection of Chuck because he was becoming a typical, morally questionable spy like Shaw and thus her solution is to chew out Chuck and…go with Shaw? What? Well, here is the thing. Sarah is not choosing Shaw over Chuck in 3.08 Fake Name. She’s choosing Shaw as a rebound because Chuck is gone, with his decision to be with Hannah and to pursue his spy career over being with Sarah. And Sarah is not choosing Shaw over Chuck in 3.12 American Hero. She’s choosing to go back to her old ways (being nothing but a spy) because Chuck’s moral compromise in killing the mole has also killed her only hope of redemption.
Sarah’s behavior in season 3, episodes 1-13 is perfectly rational and rooted in what we see in the first two seasons. Chuck is a double-redemption story. Sarah’s competence redeems Chuck from a purposeless life, and Chuck’s innocence redeems Sarah from a dehumanizing life. In S1-2, Chuck helps Sarah come to the realization that she wants a normal life, a family, kids (she tells so to Casey in 1.11 Crown Vic and to Carina in 3.02 Three Words). The obstacle was always her job, and she subconsciously rejects that at the end of 2.16 Lethal Weapon when she rejects Cole (whose larger-than-life heroism symbolizes the glamorous aspect of the spy life) and consciously at the end of 2.20 First Kill when she chooses Chuck over government orders.
Then Chuck re-intersects at the end of 2.22 Ring out of his strong sense of duty (Chuck always does the right thing) and, when given the opportunity, decides to become a spy to help others. This sends Sarah into a tailspin. Unlike Chuck, who at this point only sees the pros of becoming a spy (a life of adventure), she fully knows the dehumanizing effects of this life and the moral compromises it entails, where moral decisions become more and more grey (as she tells Chuck in 3.10 Tic Tac) and the very last thing she wants is for the man she loves to go down that path, not only for his own good but also for hers, since she’s now left a work of redemption in progress, stuck between two worlds—the reality of her spy life and her desire for a normal life. So, as the daughter of a con man always on the run, she does the only thing she knows: she asks him to run away with her. (And before we judge her harshly for this decision, we should consider the alternative she saw: her innocent Chuck turned into a remorseless Intersect 2.0 killing machine, like Chuck on Laudanol or like the two GRETAs from 4.18 A-Team. She couldn’t bear that.)
But Chuck’s acceptance of his hero calling makes him reject her offer in Prague and this starts her own journey in 3.1-12. This is a passive journey for her, by design, and we know this because when Sarah is introduced at the beginning of 3.01 Pink Slip, the song that plays in the background is Wait It Out, which underscores the nature of her 3.1-12 journey to a real life.
She was Chuck’s savior in the first two seasons but this season she will have to wait for Chuck to undergo his own hero’s journey full of trials (3.5-8) and redemption (3.9-10) and more trials (3.11) and become her savior (spiritually at the end 3.12 American Hero and physically in 3.13 Other Guy).
So, in her passive 3.1-12 journey, everything that Sarah does is a reaction to what Chuck does. He stands her up in Prague? She acts like a scorned woman in 3.1-2. He tells her the noble reason why he didn’t run away with her in Prague (Carina’s video at the end of 3.2 Three Words)? She forgives him but she can’t act on her feelings (3.03 Angel de la Muerte). He stands up to Shaw at the end of 3.04 Operation Awesome by saying nothing is more important to him than friends and family? She gives him a hopeful look at the dinner table. He starts going through his own moral compromises (First Class through Fake Name)? She freaks out. Chuck is losing himself and she, his work of redemption in progress, desperately needs to find herself. But she’s an introvert with no friends. The two people she tried to talk to (Casey and Carina) brushed her off. But Shaw listens, he understands (he lost his wife to the spy world), and so she desperately tries to connect with him and, as Morgan says of himself in 4.09 Phase Three, she overshares in order to connect. That is the whole point of her telling Shaw her real name. She desperately needs someone to talk to and share real with and she thinks that Shaw is that person.
But Chuck overhears her words to Shaw and starts on his path of redemption. He breaks up with Hannah because it’s the right thing to do, stands up for Morgan against Shaw in 3.09 Beard and then decides to save Casey in 3.10 Tic Tac. Sarah makes sure he understands the implications. If caught, he’ll never become a spy. He knows and still wants to proceed. She notices. Chuck still chooses friends and family over becoming a spy, at great personal cost. He’s not changed after all, and she admits that to him as they prepare to save Casey. So, in 3.11 Final Exam, when Chuck’s possibility of becoming an agent is very real and he asks her to give him a second chance, she implicitly accepts by leaning to kiss him.
Then the red test happens. She thinks Chuck killed the mole and concludes Chuck has changed after all—he has chosen to become a spy over his moral principles. That’s it. She’s moving on and going to Washington, away from Chuck.
Then Chuck plants seeds of doubt in her mind about what happened with the mole and, for good measure, risks his life to save Shaw, finally steamrolls through her emotional barriers by declaring his love for her and, now that he understands what she was trying to protect him from back in Prague, he’s the one who asks her to quit everything and run away with him, in a scene that is the mirror of the Prague one.
Then she finds out from Casey that Chuck didn’t kill the mole. The innocent Chuck she loved (the thesis) and who she was afraid was going to become a ruthless and morally ambiguous spy like all the others (the antithesis) has managed to become the innocent spy (the synthesis), the best of both worlds, the one possibility she hadn’t envisioned back in Prague. And with that, at the end of 3.12 American Hero, her dark night of the soul is finally over and she’s all in for Chuck.
Add that Chuck saves her life twice (warehouse and Paris) in 3.13 Other Guy and he’s not just the man she loves but also her hero and savior, her true type, and her equal with whom she can have a real relationship based on love and trust. By retaining his innocence while becoming a spy, Chuck has made possible what Sarah thought impossible—spies can fall in love.