A/N - I feel like I'm going to break everyone's hearts with this chapter. This one is a longer one.

The Doctor and Elise stepped out the TARDIS to find little black cubes everywhere.

The Doctor picked one up. He turned to Elise with a smile. "Well this is new."

They met up with Amy, Rory, and Brian.

The Doctor was now walking around the console examining the cube in his hand. "All absolutely identical. Not a single molecule's difference between them. No blemishes, imperfections, individualities."

"What if they're bombs? Billions of tiny bombs? Or transport capsules maybe, with a mini robot inside. Or deadly hard drives. Or alien eggs? Or messages needing decoding? Or they're all parts of a bigger whole. Jigsaw puzzles that need fitting together," Brian suggested.

"Very thorough, Brian. Very, very thorough. Well done. Stay here. Watch these. Yell if anything happens," the Doctor said, placing his cube on top of the one Brian was holding.

"Doctor, is this an alien invasion? Because that's what it feels like," Amy told him.

"There couldn't be life-forms in every cube, could there?" Rory asked.

"I don't know. And I really don't like not knowing," the Doctor said.

They stepped out into Amy and Rory's lounge and the Doctor made his way into the kitchen. "Right, I need to use your kitchen as a lab. Cook up some cubes. See what happens."

"Right, I'm due at work," Rory mentioned.

"What? You've got a job?"

"Of course I've got a job. What do you think we do when we're not with you?"

"I imagined mostly kissing."

"I write travel articles for magazines and Rory heals the sick," Amy told him.

"My shift starts in an hour. You don't know where my scrubs are?" Rory asked.

"In the lounge, where you left them."

The Doctor went to work constructing whatever it was he was going to use to experiment on the cubes. "Ah, the Ponds, with their house and their jobs and their everyday lives. The journalist and the nurse. Long way from Leadworth," the Doctor said, sonicing his device.

"We think it's been ten years. Not for you or Earth, but for us. Ten years older. Ten years of you, on and off," Amy said.

"Look at you now. All grown up."

The front door was busted down and heavily armed people entered the house.

The Doctor pulled Elise behind him and Amy stepped closer to the Doctor.

"Clear! Trap one, kitchen secured."

"Trap three, back garden secured."

Rory was lead into the kitchen at gunpoint. "There are soldiers all over my house, and I'm in my pants," he said.

"My whole life I've dreamed of saying that, and I miss it by being someone else," Amy quipped.

A blonde woman entered the house. "All these muscles, and they still don't know how to knock. Sorry about the raucous entrance. Spike in Artron energy reading at this address. In the light of the last twenty four hours, we had to check it out, and the dogs do love a run out. Hello. Kate Stewart, head of scientific research at UNIT. And with dress sense like that..." She pulled out a scanner and held it up to the Doctor. "You must be the Doctor. I hoped it would be you."

Kate frowned. "We seem to be missing someone."

The Doctor reluctantly stepped aside, revealing Elise behind him.

"Ah, hello there."

The Doctor stepped back in front of Elise. The Doctor wasn't too keen on all these heavily armed soldiers around his daughter. "Tell me, since when did science run the military, Kate?"

"Since me. UNIT's been adapting. Well, I dragged them along, kicking and screaming, which made it sound like more fun than it actually was."

"What do we know about these cubes?"

"Far less than we need to. We've been freighting them in from around the world for testing. So far, we've subjected them to temperatures of plus and minus two hundred Celsius, simulated a water depth of five miles, dropped one out of a helicopter at ten thousand feet and rolled our best tank over it. Always intact."

"That's impressive. I don't want them to be impressive. I want them vulnerable with a nice Achilles heel."

"We don't know how they got here, what they're made of, or why they're here."

The Doctor picked one up and tossed it in the air. "And all around the world, people are picking them up and taking them home."

"Like iPads have dropped out of the sky. Taking them to work, taking pictures, making films, posting them on Flickr and YouTube. Within three hours, the cubes had a thousand separate Twitter accounts."

"Twitter?"

"I've recommended we treat this as a hostile incursion. Gather them all up and lock them in a secure facility. But that would take massive international agreement and co-operation."

"We need evidence. The cubes arrived in plain sight, in vast quantities, as the sun rose. So, what does that tell us?"

"Maybe they wanted to be seen. Noticed," Amy said.

"Or more than that, they want to be observed. So we observe them. Stay with them round the clock. Watch the cubes, day and night. Record absolutely everything about them. Team cube, in it together," the Doctor said. He kissed the cube and smiled.

Four days later and the cubes hadn't done anything.

The Doctor was currently hanging upside down on Amy and Rory's couch, while Elise sat by the window. "Four days. Nothing! Nothing!" He picked up one of the cubes and started hitting it. "Not a single change in any cube anywhere in the world. Four days, and I am still in your lounge!" He sat up.

"You were the one who wanted to observe them," Amy told him.

"Yes, well, I thought they'd do something, didn't I? Not just sit there while everyone eats endless cereal!" The Doctor jumped up from the couch.

"You said we had to be patient," reminded Rory.

"Yes, you! You, not me! I hate being patient. Patience is for wimps." The Doctor threw himself back on the couch. "I can't live like this. Don't make me. I need to be busy."

"Fine! Be busy!" Amy yelled, "We'll watch the cubes."

The Doctor jumped up from the sofa and started to get things done around the house.

"How are you not bored?" Rory asked Elise.

Elise shrugged. In truth, she preferred the quiet. She could let her mind wander.

The Doctor soon threw himself back onto the couch. "That's better. Nothing like a bit of activity to pass the time. How long was I gone?" he asked.

Rory checked his watch. "Uh, about an hour."

"I can't do it." The Doctor jumped over the back of the couch and went inside the TARDIS.

"Where are you going?" Amy asked.

Amy, Rory, and Elise followed him into the TARDIS.

"Brian, you're still here," the Doctor said, finding Brian in the jump seat.

"You told me to watch the cubes."

"Four days ago."

"Ah! Doesn't time fly when you're alone with your thoughts?"

"You can't just leave, Doctor," Rory told him.

"Yes, of course I can. Quick jaunt, restore sanity. Ooo, hey, come if you like."

"They can't just go off like that," Brian said.

"Can't they? Can't you? That's how it goes, isn't it?"

"I've got my job," Rory said.

"Oh yes, Rory. The universe is awaiting, but you have a little job to."

"It's not little. It's important to me. Look, what you do isn't all there is."

"I never said it was." The Doctor looked at Amy, but she just stood there. "All right. Fine. I'll be back soon. Monitor the cubes. Call me. I'll have the TARDIS set to every Earth news feed. Come along, Elise."

"I'm staying," she told him. Her statement stopped everyone in their tracks.

"Ellie..."

"I want to stay with Amy and Rory. I like not having to run for my life or wondering who's gonna die."

"Oh, okay then." Elise walked over to him and put her hand on his cheek. "It's not forever. Just a few weeks. Just like when you sent me off with River."

The Doctor smiled softly. "I'll miss you."

"I'll miss you too. I just need to grab a few things from my room." The Doctor managed to keep it together long enough for Elise to pack a suitcase and say goodbye. The minute he set the TARDIS in flight, he broke down. He should have known she'd leave.

They always did.

Elise settled into life with the Ponds quite well. Their friends got used to seeing Elise around the couple.

Amy and Rory had come up with the story that Elise was Rory's niece who needed a place to stay while attending university.

Amy loved having Elise around the house and enrolled her in art classes.

Amy and Rory treated Elise more like a daughter than a friend; Elise becoming a surrogate 'Melody' for them both.

"Goodnight, Elise," Amy said.

"Night," Elise said and closed her bedroom door. She'd been with Amy and Rory for about a month now, but she missed her father and River.

Amy and Rory were great and all, but they weren't the Doctor.

She spent her days sketching and painting. Amy and Rory tried to convince her to sell some of her paintings, but Elise refused so they kept getting moved into the garage.

Eventually one month turned into two and soon it was Christmas.

Amy and Rory noticed a change in Elise. The happy girl who had first moved in with them turned into a girl who spent all her time in her bedroom, sketching in her sketchbook. Even the allure of Christmas presents and Christmas dinner could make Elise come out of her room.

Amy burst into her room.

Elise was laying on her bed, staring at a picture of herself, the Doctor, and River taken on a past Mother's Day.

"That's it. Get up. I'll not have you moping!"

Elise rolled away from her.

Amy sighed. "Elise, I know you miss your father, but you can't keep doing this."

Elise ignored her.

"Have you tried calling him?"

"He won't pick up the phone. I can't even get in touch with River!"

Amy heard Elise's voice crack and she soon dissolved into tears. Amy quickly embraced the girl, holding her tightly.

Elise didn't think it would be this bad. She thought she'd like being stationary. She did, but she missed her father more.

The New Year rolled around and Elise's attitude started to improve.

Amy and Rory made sure to get her out more often, instead of just leaving her in the house with Brian all the time. She got back into painting and even started writing in her journal again.

Soon, Amy and Rory's wedding anniversary rolled around.

Amy had purchased Elise a new blue dress for their summer barbeque, reminiscent of the one she wore to their wedding. Amy even taught Elise how to put on makeup and did her hair.

Amy was leaving yet another message for the Doctor. "Hey! Doctor, it's me. Hello. So, the UN classified the cubes as provisionally safe, whatever that means, and Banksy and Damien Hirst put out statements saying the cubes are nothing to do with them. And the cubes, well, they're just here. Still. What's it been, nine months? People are just taking them for granted. Maybe we'll never know why they came. But anyway. Elise is doing better. Personally, Rory and I just think she was going through her rebellious teenage phase. I remember how I was when I was her age, but let's not get into that. I got to Laura's wedding. It was great. She's here tonight, being as it's our wedding anniversary. We thought you might have dropped by. I left you messages."

The Doctor appeared behind her, holding a huge bouquet of flowers. "I know! Happy anniversary! Come with me. And bring your husband. Where's Elise?"

Amy pointed over to where Brian stood.

Elise looked...beautiful. He almost didn't recognize his own daughter.

Elise finally looked over at him and dropped the drink in her hand. She ran over to him and threw her arms around his neck. "Please tell me this isn't a dream."

The Doctor smiled. "You're completely awake, Ellie."

"Good, because I'm never leaving you for that long again."

The Doctor tried taking Amy and Rory on one trip as a gift for their anniversary and things kept going wrong and soon it had been two and a half months.

They returned on Amy and Rory's anniversary, but no one but Brian noticed that they were in different clothes. Even Elise.

As Elise settled in for the night, the Doctor entered her room.

"Can I talk to you?" he asked.

"Um, yeah."

The Doctor sat down next to her on the bed. "I've decided I'm staying." "What?"

"I miss Amy and Rory. And I missed you most of all."

"I missed you too."

The Doctor reached out and wiped a tear off Elise's cheek, causing her to break down.

She'd cried so much in the last nine months, it was a wonder she still had tears to cry.

"Shhh, it's okay. I'm here now," the Doctor cooed, rocking gently, "Why are there so many songs about rainbows and what's on the other side...?"

The song wasn't enough to calm Elise like it normally did.

The Doctor felt bad that he was causing her all this pain and that he couldn't take it away. He worried for what it would do to Elise in the end.