What if Chuck and Sarah had boarded that train in Prague? Some viewers say that season 3a (the first 13 episodes) are a useless misery arc and that Schwartz and Fedak also implicitly repudiate these episodes because they make Chuck and Sarah board the train in Paris in 3.14 Honeymooners as if season 3a had never happened.
I think these viewers miss the point. It is true that Chuck and Sarah board that train in Paris and run away together just as Sarah wanted to do in Prague. But notice what happens—they can’t run away from themselves, from their heroic nature. The very moment they toast their decision to quit the spy life, they are immediately prompted by their sense of duty to individually pursue the Basque terrorist and are turned on when they find out the other has been doing the same.
The very same thing would have happened in Prague. They would have been caught and they couldn’t really have run away from themselves because they are duty-bound heroes at heart. But if they have been boarded that train in Prague, there would have been a crucial difference: at the time, Sarah saw a dichotomy between her innocent non-spy Chuck (the thesis) and ruthless spy Chuck (the antithesis), the Chuck we see from 3.06 Nacho Sampler to 3.08 Fake Name, who appears to actualize Sarah’s deepest fears. By the time we get to 3.12 American Hero, however, Sarah knows that Chuck is now the synthesis (innocent spy Chuck), the best of both worlds, the third option she had never envisioned in Prague. She knows Chuck has been tempted and subjected to the ultimate moral test (his moral principles versus his spy ambition plus the allure of being with Sarah), and his moral principles have won. She now knows that he is never going to lose his chuckness, so when she finds out that he really wants to be a spy, she’s 100% turned on without any worries. If they had run away together in Prague, however, she would have still been worried that he might become a spy like all others (the antithesis to her Chuck).
Oh, one other crucial difference: Chuck did not feel like a James Bond spy equal to Bryce or Cole in Prague.
After 3.12 American Hero, he does.
And he is.
That is the reason the journey of season 3a is necessary.