Chapter 12 – A Good Man Goes to War: Part 2

James was still pacing nervously by the TARDIS, knowing that Kovarian had been far too complacent for all of the trouble that they'd gone through for this to really be over. But everyone else was happy and celebrating, so there wasn't much else that he could do.

Amy rushed out of the TARDIS, carrying a crying baby Melody.

"Hey, what's wrong?" Rory asked her.

"She doesn't like the TARDIS noise. I asked him to turn something off, but it was all, 'but I don't want to punch a hole in the space-time continuum,'" she grumbled.

"That's not the problem, Amy," James called to her, but she ignored him.

"Rory, James! The Judoon have arrested all of the Clerics in the quadrant, Jack and Pete are escorting the Silurians back home, and the entire base has been cleared," Jenny told them. She was the wife of the Silurian named Vastra that had helped them. They had been living in Victorian London and working to solve crimes in the area. "Is she alright?" she asked, looking at the crying baby in concern.

"Yes, she's just crying," Amy replied and bounced the upset child around soothingly.

"Give her to me, human fool. She needs changing," Strax demanded.

"I just changed her. I think she might need a feed," Amy told him.

"A feed, of course. I'll take care of everything," Strax insisted, again reaching for the infant.

"Er, I really don't think you will, actually," Rory protested, not liking the idea of this alien seeing his wife's breasts.

"I have gene-spliced myself for all nursing duties. I can produce magnificent quantities of lactic fluid," Strax informed them proudly.

"Oh, knock it off, all of you!" James interrupted. "She's sleepy. Aren't you, sweetheart?"

"Here we are!" the Doctor announced as he exited the TARDIS carrying a blue, wooden cot.

"What's this?" Amy asked him.

"Very pretty, according to your daughter," the Doctor cooed at Melody.

"It's a... it's a cot," Rory stuttered.

"Of course it's a cot. Give her here, Amy," James said and rolled his eyes. She handed the infant to him and he rocked her gently before placing her in the little bed. He spun the mobile of gold stars and planets over her as he sang a lullabye to her quietly.

Vastra called to them over the PA system, "Doctor, we need you in the main control room."

"Be right there!" he shouted loudly. "Things to do. We've still got to work out what this base is for. We can't leave until we know," he added in explanation to the others.

"But this is where I was? The whole time I thought I was on the TARDIS, I was really here?" Amy asked.

"Oh, Amy," Rose sighed and hugged her tightly. "Remember what I said about the other Doctor. Your thoughts and memories define who you are. Your mind was with us, which means that you were with us too."

"Your heart, your mind, your soul, were with us on the TARDIS. But physically, yes, you were still in this place," the Doctor added.

"And when I saw that face looking through the hatch, that woman looking at me?" Amy asked.

"Reality bleeding through. They must have taken you quite a while back. Just before America," the Doctor explained.

"So, her Flesh avatar was with us all that time. But that means they were projecting a control signal right into the TARDIS, wherever we were in time and space," Rory realized.

"Yeah, they're very clever," the Doctor agreed.

"Who are?" Amy wondered.

"Whoever wants our baby," Rory told her.

"But why do they want her?" Amy questioned.

"Exactly," the Doctor said with a look at James.

"Time for a chat, dad?" James suggested and they walked together back to the control room.

When they arrived in the control room, they found Mickey typing on the computer system. The screens displayed all of the files regarding baby Melody.

"You've hacked into the system?" James asked and looked at the various tests they had done on her.

"Easy peasy," Mickey replied. "Some weird stuff in here though."

"What do you mean?" the Doctor questioned.

"One simple question, is Melody human?" Vastra asked him.

"Sorry, what? Of course she is. Completely human, what are you talking about?" the Doctor stuttered.

"Not exactly, dad. I need to see how they did it," James told him and began digging further into their databanks.

"How they did what?" the Doctor asked him. "She's human. She's Amy and Rory's daughter."

"Trust me, dad, she's more than human," James replied.

"You've told me about your people. They became what they did through prolonged exposure to the time vortex. The Untempered Schism," Vastra insisted.

"Over billions of years. It didn't just happen," the Doctor protested.

"So how about him then? 'Cause he should be half human, but he seems to be about as alien as you are," Mickey wondered.

"Time Lord TNA is dominant. Any child of a Time Lord will be completely Time Lord. But I didn't... do THAT with Amy! What are you suggesting?!" he explained, completely flustered.

"That's not it, dad. Do we know when she was conceived?" James asked pointedly.

"How would I know? It's not like we talk about those things on the TARDIS. The rooms are very far apart for a reason, you know!" the Doctor protested.

"Ok, but knowing how much they're on board the TARDIS, it's likely that she might have been conceived while the ship was floating in the vortex," James deduced.

"But you can't just cook yourself a Time Lord!" he argued.

"Of course not, but you gave them one hell of a start, and they've been working very hard ever since," Vastra told him.

"Can she regenerate?" Mickey asked.

"No, she would have to look into the vortex, if it would even work," the Doctor responded confidently.

"She has," James told him quietly.

"What?" his father asked.

"Could the rest of you go back to the TARDIS, please? I need to talk to my dad for a minute," James asked.

Mickey and Vastra left to join the others back at the time ship. The Doctor and his son gazed at each other for a long moment.

"Care to explain?" the Doctor prompted.

"I know who the baby is. She isn't safe, but there isn't anything else that we can do for her right now," James said with an exhausted sigh.

"You said she can regenerate, how do you know this?" he asked.

"Because I took her to the room in the TARDIS and I saw her regenerate. She was the little girl in America, dad. When I left the orphanage, I got her out of there and took her someplace safe," James explained.

"But she's here!" the Doctor protested.

The screen in front of them suddenly sprang to life with the image of Madam Kovarian. "I see you've accessed our files. Do you understand yet? Oh, don't worry, I'm a long way away and not with the Judoon either. But I like to keep tabs on you. The child, then. What do you think?" she taunted them.

"I'll ask you again, why are you doing this?!" James shouted at her angrily.

"She is Hope in this endless, bitter war," she snarled.

"What war? Against who?" the Doctor asked.

"Against you, Doctor," she replied.

"A child is not a weapon!" the Doctor protested.

"Oh, give us time. She can be. She will be, won't she Jamie?" she smirked.

"Shut up! Just shut up!" James cried, angry tears leaking from his eyes.

"Except you've already lost her, and I swear I will never let you anywhere near her again!" the Doctor argued, placing a supportive hand on his son's shoulder.

"Oh, Doctor. Fooling you once was a joy, but fooling you twice, the same way? It's a privilege," Kovarian gloated and closed the communication.

"Oh my god!" James shouted and ran to the door, only to find it locked.

"Get back here, please! We're under attack from the Headless Monks!" Rose called to them telepathically.

"Get it open!" the Doctor insisted as they both fumbled with their sonics to decrypt the code on the lock.

"I'm trying! Oh, my love," he sobbed.

"What?" the Doctor gasped, still not grasping why his son was so enthralled with this little girl that he had rescued from the Silence as a child.

"Mum, the baby isn't real. She's a Flesh avatar, just like Amy was. They've still got baby Melody," James told her frantically as they finally got the lock open and ran towards the others.

When they finally made it back to the TARDIS, Rose was comforting Amy, who was covered in the white liquid from the Flesh avatar that had been her baby. The Doctor and James knelt next to her.

"Oh, Amy, I'm so sorry," the Doctor sighed.

"I promise you, that she will be alright," James told her.

"What are you hiding, Jamie? You know something. You knew something all along, but you never told us anything. You never stopped it before it all went to hell!" Amy accused him.

James looked at her with tears filling his eyes. He had wanted nothing more than to change it, to keep River from her tortured childhood, but he couldn't.

"Jamie, there's someone who wants to speak to you," Vastra called, interrupting their argument temporarily. "Her name is Lorna. She came to warn us," the Silurian explained as she led him to where the young woman was dying in Mickey's arms.

"Hello, Lorna," James greeted her.

"Jamie Tyler," she gasped breathily.

"Thank you for helping my family today," he said sincerely.

"I met you once, in the Gamma Forests, with your uncle," she admitted.

"Oh, I was so young then. Pirates, wasn't it?" he asked. She nodded in confirmation. "I remember. You were young then too. And we ran, didn't we, Lorna?"

She nodded silently and her eyes clenched shut a moment before her body went limp.

"Who was she?" the Doctor asked behind him.

"A girl that Uncle Jack and I helped a long time ago," he replied sadly.

"So, what now? They'd almost certainly have taken her to Earth. Raise her in the correct environment," Vastra suggested.

"Yes, they did. And it's already too late," the Doctor responded sadly.

"You're giving up?" Rose questioned disbelievingly.

"No, mum, that's not what he means," James told her.

A flash of light told them that someone had arrived via vortex manipulator and they all turned, expecting to see Jack or Pete returning. Who they saw instead was River Song.

"Oh, River," James cried and ran into her arms, hugging her tightly and sobbing into her shoulder.

"Where the hell were you today? Jamie said you'd meet us here, it's not like you couldn't have set your coordinates a little earlier," the Doctor shouted.

"I couldn't have prevented this," River told him.

"With all of your knowledge about our future? I know we can't cause paradoxes, but this is horrible!" Rose argued.

"She couldn't change any of this, mum, and neither could I. I'm so sorry, Amy. You have no idea how much I wanted to change all of this. More than anything I've ever wanted to change in my entire life, I wanted to prevent this, but I couldn't do it," James raged until River pulled him in close again and rubbed his back soothingly.

"Who are you, River Song?" the Doctor questioned, already having a clue based on James' behaviour.

River looked nervously between the Doctor, Rose and her parents. James squeezed her tighter in support, encouraging her telepathically as best he could with their partial bond.

"I'm Melody. I'm your daughter," she added looking at her parents lovingly. They still didn't know it all, but they would know very soon. "This is for you, love. Come find me," she whispered to James as she handed him a slip of paper with time and place coordinates in Leadworth. She had promised that she would guide him to the right place to pick her up and she was fulfilling that promise.

"I'm on my way," he replied and held her face in his hands as he kissed her, then ran into the TARDIS.