Poking the Flames
This is still in "The Almost People" and shows a little bit of the aftermath after the Doctor turns Amy into a puddle of Flesh goo.
"Doctor, I am frightened," Amy said, eyes confused and filling with tears, "I'm properly, properly scared."
"Don't be," the Doctor replied, trying to console her. She wouldn't have anyone to comfort her for awhile after this, "We're coming for you, I swear. Whatever happens, however hard, however far, we will find you."
"I'm right here," she whispered.
"No, you're not." He couldn't stand this. He didn't want to send her away to some unknown hell to face her kidnappers while going through labor. He was so filled with guilt. How could he let this happen to her? Why didn't he protect her better? "You haven't been here for a long, long time."
The Doctor pointed his sonic screwdriver at her, knowing this would be for the best. He'd find her. He'd save her, just like he always had. Then, Amy melted into a puddle of Flesh, leaving the two men that loved her most in this universe behind in shock and sadness.
"Amy? Amy!" Rory cried, running over to the puddle of ooze that was once his wife, falling to his knees, "No! No! What happened? Tell me what happened, Doctor!"
The Doctor stood in the same spot, sonic still in the air, frozen except for his chest moving up and down from the breaths that would surely turn into sobs if he didn't make an effort to hold it all in. "That was a Ganger, more or less. Much more advanced than what we saw today," he explained, slowly lowering his arm, "Amy was seeing it, controlling it. It was more like a Flesh avatar if you will."
"Where is she now?"
"I don't know exactly," the Doctor admitted, "But wherever she is... She's giving birth to your child, alone, with only strangers there to do with her what they will."
"Why'd they take her? What are they going to do with her?" Rory asked, frantically, tears running down his cheeks.
"I can't answer any of those, Rory. But I promise. We will find her. And when we do, whoever took her is going to be very sorry that they messed with a friend of the Doctor's." He was so angry, so angry with himself for putting her in danger like that, angry that Rory couldn't protect her better when the Doctor left them, angry that he left them in the first place, angry with whoever was stupid enough to kidnap his Amelia Pond. Someone was going to pay.
A FEW HOURS LATER...
Once Rory had wiped his tears, he headed off to bed to escape reality and be with Amy in his dreams. But the Doctor, try as he might, couldn't go to sleep so easily. He knew what would be in those dreams: only nightmares showing the possibilities of what was happening to Amy, all because of him. He could already hear the Dream Lord cackling in the back of his mind.
Instead, he paced circles around the console, drinking piping hot green tea. Yes, green tea. Every sip disgusted him, but he couldn't help it. She needed to be around somewhere, even in the form of a mug. He stared at the puddle of Flesh, which still sat on the floor near the TARDIS' entrance. Neither Rory nor the Doctor were willing to clean it up just yet.
The worst part, aside from his hurt ego, was the lack of knowledge of the situation. The Doctor didn't have a clue on who was behind this, making Amy's survival chances unknown as well. Once again, someone the Doctor loved was in danger, and it might just be his fault.
"I'll find you, Amy Pond," he muttered to himself, throwing back the last of that disgusting drink, "No matter where you are. They'll pay." And while the Doctor poked the flames of his anger, Melody Pond was born into the world, the first half-Timelady to be born in centuries.