AChuck fan recently wrote, “This is probably the most unpopular opinion for Chuck fans but I never bought Chuck and Sarah as a couple. Someone like Sarah it seems like wouldn’t be all doe-eyed over a guy, which is not to say I think she’d be emotionally dead inside just that her choice of relationships would probably be a bit more pragmatic. And she’d be able to compartmentalize things more. I just couldn’t see her going for a guy like Chuck. She might like him, care about him, admire him, or even be attracted to him physically, but I just couldn’t believe someone like her would seriously fall in love with a guy like Chuck. Later after he got to be a spy it seemed like, ok, yeah maybe, but before when he was a dorky college dropout working at the Buy More.”
I don’t consider this opinion unpopular at all. After all, it’s the same objection that seasons 1 and 2 have, that I myself had when I first watched season 1, and that Chuck himself voices to Sarah in his speech at the end of 2.03 Break-Up. He’s basically telling her, “Who are we kidding? We don’t belong together. You quell revolutions with a fork while I play video games with Morgan.” Chuck is going to the heart of the matter, nothing to be surprised about since he’s got the hands of a surgeon and his future brother-in-law specializes in cardiothoracic surgery.
Sure, Chuck and Sarah are attracted to each other—he’s tall, dark, and caring and she’s a gorgeous, sophisticated woman but what combo is a Jim Halpert with a Sydney Bristow? They like each other well enough but that may only be because they are forced into close proximity by the handler-asset relationship and because of the too many other spurious factors that color their season-1-and-2 dynamic—the cover relationship, Sarah’s sense of duty to protect Chuck and his innocence (which colors even her decision to run away with him in Prague), Chuck’s need of Sarah’s protection. the lack of freedom to pursue more “pragmatic” partners like Lou or Cole. In season 1, Lou is everything Chuck is looking for but he’s just not free to look. In season 2, Sarah’s attracted to Cole but she’s not the kind of girl who cheats on her cover boyfriend. Additionally, does Sarah love Chuck the person or does she love Chuck’s innocence and transparency since her life has always been a con or a cover? And does Chuck love Sarah the person or does he love her competence since she’s the best of the best in her field while he feels like a loser?
You see the problem(s)?
This is where season 3 comes in and why I think it’s wrong for people to say that this season is an unnecessary extension of Chuck and Sarah’s will-they-won’t-they dynamic. The season is there precisely to address all the above issues and more (e.g. feelings as a liability in the spy world). Season 3 systematically removes all the spurious layers that might color Chuck and Sarah’s relationship. Their real relationship? Gone in Prague in 3.01 Pink Slip. Their cover relationship? Gone with a handshake at the end of 3.03 Angel de la Muerte. Sarah’s sense of duty to protect Chuck’s innocence? Squashed by Shaw in 3.05 First Class. Chuck’s need of Sarah’s protection? Gone, as he’s the one who now saves Sarah’s life on multiple occasions. Sarah’s attraction to Chuck’s innocence? Gone during Chuck’s descent into moral compromise (3.06 Nacho Sampler through 3.08 Fake Name). Chuck’s attraction to Sarah’s competence? Gone since Sarah’s off her game most of the original season 3. The inability to pursue more pragmatic relationships? Gone with the end of their real and cover relationships. Chuck now has the opportunity to be with Hannah, a perfect S1 female Chuck and the best possible companion from the world he comes from, so that Chuck can determine if she’s still everything he’s looking for. And Sarah no longer has a cover boyfriend and is thus free to pursue a more pragmatic relationship with Shaw, a super spy like her who, just like her in season 1, does not like to experience feelings or even talk about them.
After removing all these layers and giving Chuck and Sarah the opportunity for more pragmatic relationships with people who, on paper, are their ideal partners, season 3 asks them whether they are happy.
They should be, right? Well, are they?

It’s different, isn’t it?
It looks like they need to look elsewhere for happiness. Maybe in the same direction this time.

Looking for real. Together.
The thing is that, over the course of three years, Chuck has been sarahfied and realizes that everything he was looking for in season 1 is no longer enough. And Sarah has been chuckified and realizes that being “nothing but a spy” is no longer enough. And so, after removing all the layers that colored their cover relationship during their first two years and exposing the kernel of their relationship, season 3 asks them again, “do you two love each other for who you are, not because of duty or need or covers or lack of better alternatives? Is this real love?”
And their answer is yes, yes, yes, yes.
Yes, yes, yes, yes
I really love reading you all your analysis of CHUCK. Well done and thought through. You really peel through the many layers of this show. It is because of the many layers I can watch this show over and over plus read others thoughts on the show. Keep up the good work!