This story is canon up through The Wedding of River Song.
It has not been read by a beta reader because I'm having an extremely difficult time finding one. I hope it looks alright.
The Doctor took a deep breath, readjusted his bowtie and braces, and rapped smartly on the blue front door before him. Not just blue, mind, the door was "police box blue". It had been his doing for he knew his Amelia Pond would love it. Rory, dear Rory, couldn't have changed color if he'd wanted to. Amy would never let him.
The Doctor considered knocking again, but was, in truth, a tad anxious to be there in the first place. It would be nice to just return to the TARDIS but-
"Hello, Ponds!" The Doctor beamed at the couple in the open doorway with his arms wide in presentation of himself.
"Doctor?" Amy asked in surprise. "Finally decide to show your face again, did you?"
"Yes, I did. Now, grab your coats."
"Grab our coats?" Amy replied incredulously. "Doctor, it's June."
"Yes, I know. It's why I'm here. Still need coats."
"Rory, grab our coats," Amy ordered over her shoulder.
"Wait, no! Grab our coats? You haven't invited us anywhere. I thought you said you were done taking us with you. You don't just show up and tell us to grab our coats," Rory argued in disbelief. "Today, happens to be kind of a special day..."
"Yes," the Doctor nodded exaggeratedly. "Your first anniversary is today. That's why I'm here."
"Aww," Amy cooed, "you remembered."
"No," the Doctor answered shamelessly. "I was picking up your daughter for a date and she reminded me that I'd failed to inform you that I'm indeed not dead. She then proceeded to remind me that I ruined Rory's stag night, missed your actual wedding, and set you up on the worst honeymoon ever... So, here we are," he paused a moment to gesture at the TARDIS where River could be seen peeking out the door. "We're taking you on a date."
"A date where?" Rory asked dubiously.
"If you're going to make such a big fuss of this, I could make formal invitations and come back next year," the Doctor offered.
"Rory," Amy growled.
"Fine, coats," Rory agreed as he reached into the wardrobe.
"Good. Meet you in the TARDIS." The Doctor raced back to the ship and was caught by River as soon as he made it through the door.
"Thanks, sweetie. It means a lot to them." She smiled at him in adoration. "Amy was really hurt when she thought you were dead. The way her face lit up when I told her that you weren't... You owe this to her."
"Yes, which is why I'm doing it. Plus it will be fun," he agreed.
"What will be?" Amy asked as she entered with Rory.
"It's a surprise," the Doctor insisted.
"It's ice-skating," River answered.
"You ruined the surprise!" the Doctor cried in outrage.
"It wasn't supposed to be a surprise. Rory doesn't care for surprises... at least not yours. We're going to the planet Kur-Ha for an evening of ice-skating," River informed them. "There are a lot of mineral lakes that freeze up and have festivals. It'll be like the Frost Fair all over again."
"Except no Stevie Wonder," the Doctor reminded her.
"You could sing a few bars though, couldn't you?" Amy teased the Doctor. "For the happy couple?"
"I dance, Pond, not sing," the Doctor objected. "Now, everyone in? All set? No more grouse from Rory? Let's go then."
"Why me? Why does he always pick on me?" Rory shrugged.
"You're the most sensible. He doesn't do sensible," River smirked.
"I do, too!" the Doctor protested. "How can you say that I don't?"
"Watch the controls, sweetie. You're getting kind of close to the -"
"Oh, shut up," the Doctor muttered, cutting River off before she could announce that he nearly knocked them onto another course. That woman could be so distracting. "I'll have you know-"
The TARDIS jerked suddenly, spilling everyone but the Doctor onto the floor.
"Didn't I j-?"
"It wasn't me," the Doctor snapped before River could finish her snarky comment. "S-something hit the ship."
"It wasn't me!" the Doctor cut River off again, swinging around the other side of the console in a panic. "Something hit the TARDIS. Attacked the TARDIS. Something blew a hole in my TARDIS!" The Doctor was frantic and outraged as he brought information up on the viewing screen. River darted up behind him to view over his shoulder when the power died.
"Oh, you can't be serious," Rory groaned. "Are we still in the vortex?"
"We're in space," the Doctor answered. "I'd give you coordinates if you cared. Personally I don't. I want to know what broke my TARDIS."
"We're in the vacuum of space with a hole in the TARDIS which is without power?" Rory asked with concern.
"She's not without power, she's on backup power," the Doctor corrected as he began searching through a nearby chest.
"Where did it hit?" River asked with a quiver of concern in her voice.
"Burst into the zero room, by the looks of it. Well, I say by the looks of it, but it's more like the lack of it. The zero room doesn't show up on architectural configuration indicators. Something definitely burst in, but- "
"I thought you jettisoned the zero room centuries ago," she reminded him. "Twice."
"Yes, well, when the TARDIS rebuilt herself she made a new one. She didn't exactly appreciate that my last regeneration blew apart her console room," he explained as he tossed a set of torches to Rory and Amy.
"Well, that's good," River replied optimistically, breathing a little easier. "The Zero Room is meant to contain the force of regeneration. It could surely keep whatever it is from breaking further in."
"We can hope," the Doctor spoke quietly as he tossed a torch to River and shed his tweed jacket. "But breaking through the outer shields and into the zero room... I don't like this."
"But what could do that?" Amy asked worriedly. "What could break through the TARDIS's defenses?"
"I don't know, but I'm going to find out," the Doctor grumbled as he rolled up his sleeves and flipped the switch on his torch. "Come along, Ponds."
The Doctor's steps were light and quick, but not rushed. But for the stiff set of his shoulders and the crease in his brow, he appeared unperturbed.
"Doctor, what exactly is in the zero room? " Amy asked as she followed him around yet another corner. "Did this thing that broke-?"
"Now's not the time, Amy," he replied quietly. "Eyes and ears open."
The Doctor stopped outside a vault-like circular door and paused a moment before stepping in. The room was large and dome-shaped with pinkish grey walls and was completely empty, making the gaping holes in the ceiling and floor quite easy to see.
"It's empty," Rory observed.
"Yes, it's always empty," the Doctor whispered offhandedly.
Amy stepped forward slowly and stared through the hole in the ceiling at the stars of open space. "If power fails completely, we're being sucked out, aren't we?"
"Power's not going to fail," River assured her.
"This isn't possible..." the Doctor blinked in utter confusion as his eyes moved from one hole to the other. "It's... It's just not possible. This is the zero room. It's like a pocket dimension. Things can't just go in and out. You don't smash into and through the TARDIS."
"Well, something did," Rory remarked. He was on his knees, crawling closer to the hole in the floor so that he could see down. "It's the swimming pool. Well, was..."
"What do you mean 'was'?" The Doctor strode forward and saw that whatever had broken through the zero room, proceeded through the pool and into the next room, taking the water with it.
"Oh no, I see books in the next room. Is it the library again?" Amy wondered aloud.
"No, the library was moved away from the pool to prevent that from happening again. I think that's River's room. Whatever it is, it went through it as well," the Doctor announced as he squinted harder, following the path of the torch lights with his beady eyes.
"What?" River shrieked in dismay.
"And into the next room, which would put it..." the Doctor muttered to himself, his eyes staring up at nothing in particular as he did calculations in his head. "Oh, no."
The Doctor leapt to his feet and rushed through the hallways, his companions scrambling to their feet and racing after him.
"What is it, Doctor?" Amy shouted as she struggled to catch up to him.
"Old control room! Whatever it is, it's in the old control room!" the Doctor roared.
The Doctor did not pause this time as he met his destination. He threw open the door and stared around wildly. Waves of memories washed over him as he stared up at the blue glowing column in the center of the control console and the empty jump seat at its side.
"This... we've been here before," Rory commented. "I thought that planet thing, House, deleted-"
"Shh!" the Doctor snapped. "One hole, Rory. Whatever it is, it's here. Or... not?"
He walked a circle around the room with a look of utter perplexity. There was nothing but a hole in the wall.
"B-but Doctor," Amy started tentatively. "The hole is in the wall... not the ceiling."
"You still think side to side," the Doctor answered slowly as he approached the gaping hole in the side of the room. "All lefts and rights in the hallways, yet we traveled four levels down. This hole in the wall, is River's bedroom floor. And it was the pool floor was against her other wall, as you can see by the evidence of water everywhere." The Doctor splashed lightly in the few centimeters of water that lined the floor.
"I know you want me to pout about it, but I won't," River declared loftily. "I'm more intrigued by this place. This was your last control room?"
"Rather dim and depressing..." she said as she went to poke the stained, tired chair.
"I prefer 'organic'. And the blue is mood lighting," the Doctor said defensively. "Now stop insulting my past and let's find-"
"Doctor," Amy said tentatively. "What's wrong with this wall? It's... It's like paper thin."
"What?" The Doctor stepped down from the metal grate floor and made his way up to the gap again, inspecting it closer. "This definitely isn't right... And... And there's no debris. Why didn't I notice that? All the holes and no rubble. Just water."
"Oh God! It's a hand!" Rory cried in shock. "Doctor, there's a hand! I-It's a person!"
"What?" River turned on the spot and her eyes followed his down through the grate metal flooring. Before the Doctor and Amy had even made it across the room, Rory and River had the flooring ripped up and Rory was checking for a pulse. "How did she get under here?"
"The flooring's raised," Rory answered, looking around from where he knelt with the girl's body draped over his lap. "She must have rolled under here from the momentum."
"A girl," River spoke in bewilderment. "Just a girl? A human body burst through four levels of the TARDIS? How-?"
"She's alive!" Rory exclaimed. "She-she's not... We have to get her to the infirmary. Doctor?"
The Doctor stood frozen in shock, becoming pale as he stared at the blood and water dripping from the young woman's blond hair.
"Doctor, do you know her?" Amy asked worriedly.
"Doctor!" Rory shouted to get his attention. "She's alive, but I don't know-"
"Infirmary," the Doctor whispered hoarsely to himself. He shook his head to clear his daze and swiftly scooped the girl's limp body into his arms, the wetness of her clothes immediately soaking into his.
"Doctor, she has-" River held up a black rucksack and the Doctor cut her off there.
"Rory, take the bag and follow me. Don't look in it. And careful with it!" the Doctor's words turned into shouts as he was halfway down the corridor by the time he finished speaking. Rory snatched the bag out of River's slack grip and took off after the Doctor. River and Amy followed immediately behind.
"River!" The Doctor shouted over his shoulder as they returned to the control room. "I'm going to need power, do you think you can get her going?"
"Of course, but, Doctor, who is she?" River asked.
"Her name is Rose."