I was going to have a scene where the Doctor further explains his connection to Jack. This was where he talked about the events in Children of Earth and Jack's immortality. This was to be inserted after Jack discovers the Doctor and the Doctor is rewiring stuff. I ended up coming up with a more suitable plot line so I scratched this out. It was also a bit wordy and too much explanation.

Small The Beast Below ref at the end that I liked. Also a small ref to the Doctor's unvoiced romance with Rose. Sorry Amy/Doctor shippers. I don't like it that much. Rory's cuter.

"Are you going to explain now?" Amy asked, tapping her foot.

"Saving the world, not a lot of time. Very complicated. Maybe later."

"So multitask, c'mon."

"I knew him before. He was as companion, a traveler. 51st century, like River Song, no association though. Part of the Time Agency. It's like the time police. Some stuff happened and he left them hiding out in the London Blitz. Found him while I was traveling with this other girl, Rose. He tagged alone and then we came to the Daleks."

"Like Churchill's Daleks?"

"Yes but not quite. These were the real Daleks. The Ironsides were impure, but that's not the point. The point is that Jack died."

"Yeah, but he's here right now."

"Yes, and I also mentioned that he was immortal. I sent Rose back to Earth, back to safety and she came back. Absorbed the Heart of the TARDIS to try and save us. Destroyed all the Daleks and brought Jack back forever. She couldn't control that power."

"Hold up. What do you mean the Heart of the TARDIS?"

"She's alive."

"No way really?"

"Where were you when I said that before? Did you think that a TARDIS was built?"

"Yes, I-"

"Moving on."

"Then what about the gun Doctor? He looked like he was going to kill you. What was that all about? The Silo? Utopia?"

"A long story. You don't remember it."

"Just because I don't remember anything about the Daleks doesn't mean that I don't remember anything at all."

"No I mean you really don't remember it. It was the Year that Never Was. A paradox that no remembers except for those in the eye of the storm."

"Summary then?"

The Doctor's shoulders drooped as he thought about the Master. "Harold Saxon, the PM? Remember him? I knew him as the Master. He was a Time Lord. He wanted a new Gallifrey. He'd been hiding at the end of the universe, memories erased. It was a crazy time. Refugees were hiding out in what they called the Silo. They all believed in a brand new world called Utopia.

"It didn't work out. The Master regained his memories and stole the TARDIS. When we came back, Jack, Martha and I, we missed the elections. We were public enemies of the state by Harold Saxon."

"Hang on," Amy cut in. "I've seen Jack before. On the telly! And the other girl. But that wasn't you. The other picture. You look totally different."

"Regeneration. It's a Time Lord trick. When we first met, remember that? Back when you were a little girl. I fell out of the TARDIS clutching my chest and breathed out this golden air, telling you I was still cooking? Anyway, we tried to save the world. Some things happened along the way and Saxon tortured Jack for a whole virtual year. He wasn't the same after that but he put on a good show of being brave. I fixed things up and here we are."

"Yeah, but why did he want kill you?" Amy reiterated.

"The Nyaloxo"

"What's that? You said 456. Do you mean-"

"September 2009. Yes. Children talking. The Nyalaxo are addicted to the hormones prepubescent kids produce. Like a drug. And Jack saved the world. Brave old Jack. Him and his old Torchwood team. But…"

"He lost," finished Amy.

"Everything. His lover was killed. He sacrificed his grandson and his daughter disowned him."

"Grandson?" Amy repeated. "How could, I mean, why would-"

"The star whale Amy," the Doctor said, stripping a wire and twisting it to another one. "One creature or hundreds more. One child or the children of Earth." The Doctor pocketed his sonic screwdriver and faced Amy. "He couldn't stand and watch the children cry." Amy looked back into those eyes are saw something between regret and sorrow. "He's a fixed point in time and space, a fact. Never-changing, always constant. While everything around him dies, he'll still be around. He's going to outlive even me. That kind of loss and hurt is enough to drive anyone mad."

"That's why he wanted to kill then. But he's still here," Amy said. "That's got to mean something. And you said he was like you."

"I lose everyone too, just not to death. One day, you're going to grow up even more. You'll want to start a life of your own and I have to learn to let go."

"I want to explore the universe forever."

"That's what Rose said," the Doctor replied sadly. "Years ago. Rose, sweet Rose. Lovely, lovely Rose. She's happier now."

"Did you love her?"

The Doctor merely smiled as he checked the systems so Amy decided to change the subject slightly. "Very old, very kind and very, very last of its kind?"

The Doctor looked up. "Yeah. Something like that."