The Doctor could see it. He'd seen it when she'd moved and talked, but he doubted Amy and Rory had. They didn't know the signs and probably thought it was normal for after a regeneration. The Doctor walked forward slowly. He watched as not-quite-his-River stumbled slightly.
"You're pushing your body too far." He told her, "You've only just regenerated."
"So I have a new body." River shrugged, "There's nothing wrong with me."
"Well, as I once told Harry Sullivan: a new body's like a new house, it takes a little time to settle in." the Doctor argued, "That bullet went right through your regeneration network. You almost didn't regenerate."
"What does that…" River began to ask.
She didn't get a chance to finish. Her knees buckled and she fell back with an involuntary whimper, right into the Doctor's arms. He dropped to his knees as Amy and Rory ran over. Releasing her legs, he reached over and cupped her cheek, moving her head to his shoulder. Her entire body was tense. Experimentally, the Doctor touched her temple and tensed himself.
"Doctor, what's wrong with her?" demanded Amy.
"Post-regenerative trauma." The Doctor explained, "It's very normal for this sort of situation, but apparently Madame Kovarian doesn't understand that. She's sending a wave through time and space to torture your daughter. Evidently some sort of punishment for her 'weakness'. If we can get her back into the TARDIS, we can interrupt it."
He leaned down and kissed her temple.
"Shh." He hushed her, "You'll be fine soon."
He slid his arm under her legs again and stood, lifting her. Amy and Rory ran to the TARDIS. They opened the doors for him and he carried their daughter in. As soon as the two humans closed the doors behind them, River slumped in his arms.
The TARDIS hummed in concern. The Doctor carried River out of the console room, followed closely by Amy and Rory, and into the medbay. He laid her on the bed and pulled the scanner over her.
"Well?" Amy asked anxiously.
"She'll be fine." The Doctor said, "However, something's trying to kill Hitler and while that sounds good, it could destroy time."
"We'll go out and get started." Amy said.
Amy and Rory walked out. The Doctor walked around the young version of the woman he'd fallen in love with. First he pulled the vest off her and threw it over the back of one of the chairs. Then he pulled her boots off and dropped them on the floor. Finally, he walked over and grabbed a blanket. Returning, he threw the blanket over her and wrapped it around her.
He paused and cupped her cheek again.
"You and I are the last two Gallifreyans in existence, Melody Pond." He spoke to her, knowing she could hear him, "Barring, maybe, the Master. And he's nowhere near as beautiful as you are."
He took her hand and raised her knuckles to his lips.
"Listen to me." he told her, "I'm not just telling you this to save my own skin. I teach this to everyone I love: just because someone tells you that you have to do something doesn't mean you have to do it."
He laid her hand back down.
"The TARDIS will show you what I mean while I'm gone." He promised, turning and leaving.
When it was all over, the Doctor returned to the medbay. River was sitting up, staring into space. He came over and sat at her bedside. River turned her head and looked at him.
"They told me Dani was still committing genocide."
"Not anymore." The Doctor told her, "Not since she was a child."
He could see the change in her eyes. She no longer wanted to kill him. Now, the scared girl that she really was, was displayed before his eyes. He held out his arms to her and she climbed off the bed and into his lap after a moment of hesitation, probably unfamiliar with the gesture. The Doctor rocked her and stroked her hair.
"My bespoke psychopath." He whispered.