A/N: Although I've loved every one of the Doctor's companions I've ever come across (old and new Who), the Ponds-all three of them-have remained my favorites. This is a poor tribute to their farewell, but it's all I can manage for the moment.
Also, I know I've missed a few of the times Amy and Rory lost each other, but honestly, it happens (happened...) just about every episode, so I think I can be forgiven. ;P
What God Hath Joined Together
The first time she loses Rory, she shuts down. She goes numb in disbelief, because somehow she'd always believed that Rory—maddening, stupid-faced, normal Rory—would be the one thing in her never-makes-sense life that never changed.
The grief just starts to hit her as she's starting the van, and she slams her foot down onto the accelerator in vicious anger and a little bit of fear.
She had no idea she could ever love someone enough to feel this much loss and she never wants to feel this black hole of sorrow inside of her again.
The second time she loses Rory she doesn't remember it, and when she finally does, the not-remembering feels like the worst sort of betrayal and fills her with shame that she never speaks of.
Of all the futures he's dreamed for himself and for Amy, even after they begin traveling with the Doctor and see the absolute weirdest parts of the Universe, becoming a plastic centurion from his girlfriend's memory as bait in a trap for her Raggedy Man was not in his wildest imaginings.
He worries about himself, sees the odd glances the Doctor (sneakily) tosses him, wonders what sort of a Thing he could be to come back from being erased from Time.
Amy settles that question when she says "Rory Williams—my boyfriend" and he has time to crazily think Obstinate, contrary, beautiful Amy Pond, pulling her boyfriend back from the dead before the gun in his hand goes off.
Reality implodes around him, stars wink out and the sky turns black, and all he can do is hold her in his arms and wonder how, if his heart is made of plastic, he can possibly feel this alone.
Rory has always been afraid of water, Amy thinks as he disappears beneath the surface.
After drowning, Rory teaches himself to swim. Amy has trouble ever looking at a pool again.
Rory is terrified, and it isn't even because his wife has melted into a pile of goo at his feet (because, if he's honest with himself, he's seen much stranger things). It's terrifying because she's gone, she has been gone and Rory never noticed and he realizes he's done the one thing he swore never to do and trusted the Doctor over his wife.
He remembers screaming You have no idea how dangerous you make people to themselves and remembers thinking that he could maybe forgive the Doctor for that but he couldn't forgive him, not ever, for making him willfully put Amy in danger.
She never tells Rory that the handbot had no name for almost a decade. She called it "Robot" and "Faceless" and even, for a time, "Hey you!" The burning anger she feels against the Doctor settles into cold disgust and she only ever snarls his name; but the ache that was Rory never eases and still leaves her shaking with tears she doesn't allow to fall.
She names the handbot Rory just because she needs a good excuse to shout his name every once in awhile, and the reminder of what she has lost is a double-edged sword.
They both lose each other, and this time they have no Doctors or messed-up timelines or psychopathic daughters to blame but only their foolish selves. They hold tight to one another and vow to never let go again.
At first he can't quite believe this happening again. Is this the curse of the Ponds, to do nothing but lose and find, find and lose?
He lives a life, builds a life, because someday Amy will come and he does not want her to find him weary and broken.
New York is not Apalapucia, and his grief only grows old, never morphing into the bitter hatred Amy nursed for decades, and Rory Williams is, at the end, no Last Centurion. He's just a lonely old man, afraid of dying alone, and he thinks for the first time he might understand the Doctor completely.
It is no great surprise to her that she must choose between them once again—that her Finding can only come through Losing—but she has lost them both before, and she knows which pain is greater.
She says "Goodbye!" exactly once, and never says it again.