What’s the point of the final arc of the series? Isn’t Sarah’s growth, which represents half of the show, all for naught if she loses her memories and remembers nothing of the past five years?
The memories do come back with the magical kiss—it’s a reversal of the ending of 4.09 Phase Three; the whole show is built on symmetries and counterpoint.
The point of the finale is to show that Chuck and Sarah’s love is so deep that it goes even beyond memories and that, because his love is selfless and self-sacrificial, as shown in his decision to upload the Intersect to help others on the roof of the concert hall, he deserves both the pristine version of the Intersect and the girl.
Quinn and season 5 make a metaphorical bet, kind of like the one between God and Satan at the beginning of the book of Job. Quinn taunts season 5 that Chuck could never get the girl without the Intersect. Season 5 raises the stakes by betting that Chuck could get the girl even without the Intersect, without her memories, and with her old trained-assassin self being given a kill order on him.
Chuck convinces Sarah’s head in 24 hours (5.12 Sarah) and wins back Sarah’s heart in four days (5.13 Goodbye). And with that, they are rewarded with her memories.
He wins her over again and again. And again.
That is the theme of the show.
The point of the final arc was never Quinn or his motives or his plan or Sarah losing her memories for good. Quinn is just a plot device used to temporarily reset Chuck and Sarah’s relationship and then lose his bet.
Some say the taunt is pointless because Sarah’s love for Chuck in the beginning is not due to the Intersect but to Chuck’s character. This is true but the two scenarios are different. Chuck at the beginning of the show has the Intersect and Sarah’s job is to monitor him and then protect him. Chuck at the end of the show does not have the Intersect and Sarah’s job is to kill him.
It’s also true that Sarah falls back in love with Chuck on that beach at the end of the series when Chuck has the Intersect back in his head but the reason Sarah asks for the kiss has nothing to do with the Intersect. In fact, the Intersect had lost Chuck the possibility to get Sarah’s memories back earlier at the concert hall. Sarah asks for the kiss because of Chuck’s selfless love for her displayed on that beach. We must remember Ellie’s words at the beginning of the episode, “Chuck, this is your mission. Find Sarah. Be yourself.” What wins Sarah back is not the Intersect. It was never the Intersect. It’s Chuck.
Even in the book of Job, God allows Satan to do a lot of damage to Job, just as the S5 final arc allows Quinn to do a lot of damage to Chuck. And Job wrestles with his faith just like Chuck at the beginning of the final episode (“Sarah’s gone. She doesn’t remember me. I’m no longer a spy. I’m back where I started. Alone in Burbank.”)
Sarah represents us viewers. After five years, we might have forgotten Chuck and Sarah’s journey. And so, the final episode is a synopsis of the show for our benefit. It’s Chuck and Sarah’s love story summarized in one episode.
It’s their goodbye to us and their exhortation to remember them.