A fan asked this question, “After having watched the show a lot of times, I have only now realized that Chuck tells her all that stuff about them never being able to be together in maybe an attempt to save her life, because of what Bryce had told him, which makes a lot more sense. Before now, I had never understood why Chuck did that. But what are we supposed to understand that Sarah was going to say?”
She was probably going to tell him what she had just told Casey, that she hesitated (when Chuck was held at gunpoint by the Fulcrum lady) but could still protect him. She might have also, maybe, added that they needed to scale their relationship back a little so that she could better protect him. But Chuck goes far beyond that and for the heart of the matter—they will never be together because they are not on the same ontological plane of existence; he is a normal guy while she is a super spy. Sarah is shocked and in tears and only later in Devon and Ellie’s apartment realizes that Chuck broke up with her for her sake, in order to protect her physically, emotionally, and professionally. Because of that, she loves Chuck even more and will later do the same for him at the end of 3.02 Three Words, after he decides to join her ontological plane of existence by becoming a spy.
It’s significant that the lyrics of the background song Skinny Love that come to the foreground when Sarah gets up and cries after Chuck’s break-up words are a foreshadowing of their season-3 journey:
♪And I told you to be patient
And I told you to be fine
And I told you to be balanced
And I told you to be kind
And in the morning [season 3], I’ll be with you
But it will be a different kind [because it’s not what Chuck expects, i.e. a normal life]
‘Cause I’ll be holding all the tickets♪ [Chuck will join Sarah’s world]
And after Devon’s prophetic words about Chuck and Sarah being next, when Sarah turns and looks at Chuck, we hear these lyrics:
♪Who will love you?
Who will fight?
And who will fall far behind?♪
Chuck will love Sarah and fight for her, and all other spies will fall far behind.