OH HELL YES
ONE OF THE CHARACTERS DIES.
And of course it’s Rory.
But it’s because he’s secretly The Master.
The Doctor is, of course, forced to kill him.
But Amy can’t understand. She loves him; he’s the father of her child. Hell, he waited 2,000 years for her! She reasons that Master!Rory has been with them so long, been so good, helped so much, been so true that he must be okay.
But The Doctor knows better. He knows that The Master has been biding his time, gaining power and information, honing his powers, waiting for reinforcements, watching for his opportunity. The Doctor knows that he has to kill this guy, because he’s not really Rory. Rory, in fact, never was. He was simply an idea, a character, a disguise — a way to get close to The Doctor. So The Doctor kills him; it’s the only thing to do.
But Amy can’t understand. She’ll never understand. And she could never forgive The Doctor for killing the man she loved. So she leaves. The Doctor could try to changer her mind, explain the reality of the situation, convince her to stay. But he doesn’t. After all, he’s better alone. Less vulnerable. And he’s not mad at Amy. He’s used to it, after all; they all break his heart in the end.