This was originally drafted in May 2012 after the initial set spoilers about "Asylum of the Daleks" came out. This is my theory about why River isn't there to begin with in series 7. While the episode did retcon a good bit of this, I still like the story.
"Touch my weary head, and tell me everything will be all right"
It was probably a good thing the Doctor happened to stumble into the kitchen, otherwise he'd never known that River was on board.
Well, it's not like the TARDIS monitor hadn't beeped the moment he got back, but he'd been a little too busy tearing off his trousers and waving them in frantic circles in the air to dislodge the rest of the four-inch poisonous thorns that had wound their way into the cloth. Since he'd been on M#*$ra, the thorns also happened to be imbued with a particularly vicious purple dye that now covered him from head down to the socks with dancing badgers in fezzes that he wore. He needed three cups of sugar, pure lard and bootstrap molasses, and that was just to get the stuff off him.
He strode into the kitchen, spotted River at the table, and did a double take. He paced to the door, then back, trousers dropping to the ground as he fisted his hair. "Really, River, have you been here the entire time?" He gesticulated wildly toward the console room. "There were six-feet Banraians out there! With poisonous thorns! I could have used some help."
When he didn't say any, he strode to the table, planting his hands on the wood with a thump and waited. Waited. Waited …
But his wife merely stared into her cup of tea. Her thoughts, he realized, were very far away. They had to be grave ones indeed, because River Song never passed up a chance to make fun of his clothing, leer at the lack of said clothing or laugh at his latest predicament. Concerned now, because River was being decisively not River-ish, the Doctor slid into the chair next to her. "River?" he asked gently, laying a hand on her arm and really hoped she wouldn't shoot it off in reflex.
She startled, then glanced up at him. She looked very, very tired, he realized, and much older than the still relatively young woman he'd been picking up every night from Stormcage. "Hello, sweetie," she rasped, then took a sip of tea. She grimaced. "Sorry. It's gone cold."
"When is this for you?"
She gave him a wry grin now. "You just zapped my vortex manipulator and sent me off after busting up a Sontaran hen night."
She looked far older than the sassy girl that had breezily informed him that he'd had her banged up in prison for five years. "Something happened. Something happened, didn't it? Where'd you go?"
River arched an eyebrow. "Well, instead of sending me back to Stormcage, you sent me to Leadworth. 2012. So, I visited my parents."
His gut twisted, but no, no, everything was OK with Amy and Rory. Everything was fine and good, and his Ponds were his Ponds. "The Ponds! Amy and Rory! We should pop right down to see them! I'll take you to the planet of roller coasters! Went there in my sixth incarnation with Peri. Made me a bit sick, but I'm sure I have a stronger stomach this go-round!" He glanced down. "Well, this planet requires trousers, otherwise they put you in a jail that's nothing but funhouse mirrors and mimes. Peri said the jail complemented my coat." He wrinkled his nose. "That really was quite rude."
"Sweetie. First of all, that coat was hideous."
"It was no …"
"Second, I think my parents might be getting a divorce."
He blinked at her. Just blinked. Really, River was a very sensible woman underneath the guns and explosions and flirting. She had a brain nearly as good as his own. Therefore, she wouldn't be saying this complete and utter nonsense under normal circumstances, which could mean only one thing.
"Right, off to the med bay with you!" He grabbed River's hand and tried tugging her out of her chair. "We'll find out who brainwashed you and fix you up in a mo'. Well, little more than a mo'. Need trousers first. Oh, sorry, getting that dye all on you. Right, first molasses, then trousers, then brainwash fixing."
For the first time, River took in the Doctor's predicament. "What on Earth were you doing? Tangling with Banraians?"
"I told you that, but you were too brainwashed to listen. Now, where's the bootstrap molasses?"
"Sweetie, there's a cream I can make with marshmallow fluff, Nutella and sea salt that's far more effective at getting that dye off, and I'm not brainwashed." River shoved away from the table and began rummaging through cabinets, pulling out jars and a basin.
"You, River Song, are definitely affected mentally somehow." The Doctor danced around until he was in front of her, pressing his nose to hers as he stared deep into her eyes. "Is it the Silence? Is someone making you do this?"
"No one is making me do this." River stepped around him to put the items on the counter. She started to twist the top off the Nutella, sighed and set it back down. "When I got to my parents', Amy was at the table crying. I landed some time in 2012, I didn't really check the date. She and Rory had been fighting again. And …," her breath hitched, "there were divorce papers on the table in front of her."
"That's not possible! They're Amy and Rory!"
"Yes. And they're so, so human." She pushed a lock of hair behind her ear. "Doctor, do you realize what they've been through the past few years? They lost a child, a child they can't tell anyone about. She was kidnapped, brainwashed and tortured. She was groomed into a psychopath to kill their best friend. Then she dies not once, but twice. The first was starvation on the streets of New York, and I will never tell them that and …" She suddenly found herself in his arms, covered from head to foot in purple dye.
"You starved." His voice was low and matter-of-fact, but fury laced through it in a chilling manner that made a good number of species turn and run.
"You didn't know," she murmured, and she absently rubbed his back in an effort to comfort him. "Well, malnutrition combined with pneumonia, but it was my fault. I ran away and was on my own for months and …"
"Don't you ever apologize for that." He shook her slightly. "It is not your fault. You. Were. A. Child." And the unimaginable horror was almost too much for him to comprehend. He'd been shot, fallen off a radio tower, poisoned, absorbed radiation, really if there was a guide to creative regenerations, the Doctor was its poster child. But starvation and disease. It was one of the worst ways imaginable for a Time Lord to regenerate, because the body was consumed from the inside out by the organs trying to hang on just a little longer. And his wife had done that when she was very small. He thought of the little girl begging for help from that spacesuit and … he buried his face in her curls and hated himself so, so very much.
And now, her parents - his best friends - were fighting and considering a divorce because of what happened. Because his actions led to their child being taken away and groomed into a weapon. Well, he was going to fix it. He was going to fix all of it, and Amy and Rory would always be Amy and Rory. That was a fact, as hard and fast as Jack Harkness' immortality. Rory had waited 2,000 years for Amy. They had found each other again and again through death, cracks and all of time happening at once. There couldn't be Amy without Rory, and there couldn't be Rory without Amy. End of discussion.
"Right! I'm going to fix this! No. We're going to fix it!" The Doctor grabbed the Nutella jar and sprinted toward the console room. "Quick, cover me with this and grab a paper lantern and that old Fyxlan calibrator that's under the nightstand in our room. My nightstand that is. You keep yours annoyingly neat. Oh, and I need some trousers. Mine are currently eating a hole in the floor."
"There's about 1,537 honeymoon planets I haven't taken them to yet, and we'll tag along! It'll be fun! Except when they're being mushy and snogging, and don't give me the beady eye there." He skidded to a halt and blushed, adjusting his bow tie. "What we do is private, dear."
River followed, carrying the rest of the items she pulled out. "Sweetie, no."
He paced around the console before spinning back to her. "I'm not going to let them get a divorce because of me."
"They're getting a divorce because of them." She dropped the items on the console. "They could have lost Melody … me … in a myriad of ways. It's the same way for a marriage. You can't fix things every time they go wrong."
He thought of Amy trying to use him to stave off her impending wedding and thought it wise to remain silent on that one.
"They have to live their lives and their marriage the best they can. Just like we do. And if they think that's a life better lived apart …," her voice hitched again, and she lost the struggle against her emotions. She braced herself against the console and closed her eyes. He could see the struggle to master her emotions, but there were just some things too big to handle. Even for River Song. The Doctor put the Nutella down as he approached her, and this time she turned into him and took the comfort they both needed. Her sobs were mostly quiet, and he ignored the tears silently streaming down his own cheeks.
"Right," she said with false bravado. "Let's get this stuff off both us, and you go see Amy and Rory."
"But you …"
"I don't need to be there right now." She brushed her eyes with the back of her hand, turned back to the console and began mixing up the cream. "Amy and Rory have done nothing but make me feel welcomed and loved, but they need to get through this on their own. Without me."
"It's not your fault," he murmured.
"I can't help thinking it is," she admitted. "And that's something I have to work out for myself."
No, he thought, it wasn't River's fault. Never had been. Never will be. The Silence wouldn't have wanted Melody Pond if it hadn't been for the Doctor. But because he knew that feeling of guilt and self-hatred so, so very well, the Doctor said nothing.
"If you can't go with me to see your parents now," the Doctor said much later, once they'd gone through three giant tubs of marshmallow fluff and six jars of Nutella (four for the cream and two for ... well … private matters), "will you at least go soon?"
"Count on it." Sounding far more like herself, and wearing far too many weapons to suit his comfort, River stood at the console fiddling with various monitors, keying some notes into her tablet, then consulting her diary, turning every so often to deter the Doctor from taking a peek. "I'm not in a rush to get back to Stormcage. I think I'm going to go investigate this interesting spaceship."
"Hmph. What's so interesting about it?"
"Oh … you'll find out soon enough." River smiled cheekily as her sketch of the Doctor riding a dinosaur and closed the book.