Author's Note: This is the final chapter, hope you enjoy.
Rory gripped the railing as the TARDIS flung them from side to side while heading to the co-ordinates the Doctor had entered. Finally they landed and he looked over at the Time Lord.
"Where are we?" Rory asked.
The Doctor shrugged, "No idea. Let's find out."
Rory dropped his head, "Why not check before we go out," he held up his hand, "Don't tell me. That wouldn't be any fun."
The Doctor grinned, "You remember."
Rolling his eyes Rory followed the Time Lord out of TARDIS and into a white corridor. The Doctor walked one way and then another before frowning, licking his finger and holding it in the air for several minutes.
"You have no idea where we are," Rory leaned against the wall beside the TARDIS, "Do you?"
"I'm working on it," the Doctor told him.
Rory chuckled, "Well we're in space."
"How do you know that?" the Doctor asked, surprise and irritation in his voice.
With an amused smile Rory pointed just behind the TARDIS, "Because I can see out the window."
He clearly heard the Doctor swear at him under his breath before stalking off in a random direction. Chuckling to himself Rory followed on.
x
The Doctor could taste something odd about the air in the ship/space station they'd materialised onboard. He was beginning to get a very bad feeling about this.
"Doctor?" Rory's whispered call made him pause for a moment. He turned and held up a finger to get him to be quiet.
"I hear voices," the Doctor murmured softly, "Stay completely quiet we don't want anyone else knowing we're here."
"I remember the drill," Rory replied before adding, "So make sure you don't sneeze."
The Doctor rolled his eyes but didn't reply instead moved closer to the doors at the end of the corridor. Using the sonic screwdriver he opened the doors just enough so they could see and hear inside.
"Please," a woman cried distraught, "Please don't take my baby away."
The familiar laugh sent a shiver along the Doctor's spine, "It's not your baby, my dear. He is my experiment and I must admit he came out better than I expected."
The Doctor felt Rory stiffen at his side but he managed to remain silent.
"Don't take him," the woman cried, "I will do anything."
"You will but that won't do anything to change my mind," the other occupant replied, "I am however feeling magnanimous today because of how well the experiment went I will let you have a few minutes with him."
x
"Come on, Rory," the Doctor pulled his arm the moment the other man left the room via the door at the other side, "Help the woman, do not touch the baby."
The woman was standing over a crib turning when she heard them and Rory saw the fear in her eyes.
"I'm the Doctor, this is Rory," the Time Lord quickly introduced, "We're here to help."
Rory's brain caught up with what was happening and he realised suddenly that the frightened woman was his real mother.
"Rory," the Doctor stated deliberately, "Help her to the TARDIS while I take the baby."
Nodding he slipped his arm around the woman's waist and started them moving, seeing the Doctor gently lift the child from the cot. Rory kept his focus on the woman, barely more than a girl really she looked about ages with Amy when the Doctor came back the first time.
"We're almost there," Rory assured her as they continued to the blue box.
He blinked when the Doctor clicked his fingers and the doors opened but didn't have time to think it over. Once inside Rory moved to the console, still holding the woman, waiting for the Doctor. As soon as the Doctor stepped inside, slamming the door behind him, Rory hit the button to take them home.
"Please," the woman whispered reaching for the baby.
The Doctor shook his head, "First, Rory is going to take you to the medical bay and make sure you're healthy," he held up his hand to stop her saying anything else, "Don't worry, the little one will be there while I make sure he's okay."
Rory nodded when the Doctor motioned him to go and guided the woman to the medical bay.
x
"What's your name?" Rory asked gently, helping her onto the bed.
"Lily," she whispered, her eyes darting to where the Doctor had placed the baby.
Rory smiled down at her, for the first time taking in her appearance and seeing a lot of himself in her face. Her eyes and her sandy brown hair were the same as his and he recognised the confused quirk of her lips.
"I'm Rory," he told her, "You don't have to worry, I'm a nurse. I just want to make you're okay."
She nodded turning sharply when the baby gave a cry.
"Yes, I know it was cold," the Doctor said to the child, "But I have to listen to your heart."
Lily turned to Rory confused who shook his head, "It's easier not to ask."
She gave a small laugh and Rory felt his heart clench slightly wondering how long he would get to spend with her. Quickly Rory gave her a check-up finding she was completely healthy.
"Doctor?" he turned to the Time Lord.
The man in question lifted the baby once more and rested the child in his mother's arms, "He's healthy."
"But different," Lily whispered hugging the baby close.
The Doctor nodded before finishing, "And I am sorry, Lily, I am so sorry but you can't keep him and I can't give you much time with him either."
"No," Lily cried.
The Doctor sighed, "I wish you could raise that little boy but you know that the man who did this will find you and when he does..." he trailed off, "This is the only way to protect that little boy."
Lily nodded, rocking the child as she tried not to cry.
"Doctor," Rory said, "Can't we..."
"No," the Doctor cut him off, "The baby was barely a day old when found remember and we need to get him to that rendezvous."
"But..."
"I will explain everything once we do this," the Doctor promised.
x
Rory felt ill as he watched Lily hold her child close, hold him close knowing she would never see her baby again. It was beginning to look like a family trait and he was beginning to understand how River felt when she saw them before they knew who she was.
"You need to remember that I always love you," Lily whispered to the baby, "And I know you'll be a good man when you grow up."
Feeling tears prick his eyes Rory turned away, focussing on the Doctor writing his note for them to find earlier today.
"Okay," the Doctor appeared carrying the car seat and moved to Lily, "We'll be landing in a few minutes. You have to say goodbye."
Lily was crying at this point but placed her baby in the seat whispering how much she loved him over and over. When the Doctor lifted the seat Lily gently kissed her son's forehead once more before staggering away. Automatically Rory caught her and wrapped his arms around Lily while she cried on his shoulder. He continued to comfort his real mother while the Doctor left the baby on Sarah-Jane's doorstep.
When the Doctor reappeared he went straight to the console and hit a few buttons before turning back to them.
"I think it's time we all had a conversation," he said.
x
The Doctor placed a mug of tea in front of Lily while Rory took his own, they'd relocated to his office and the chairs sat in a small circle for this discussion. The new knowledge of Rory's true origins was staggering but he had to deal with the young woman first.
"You seemed unfazed by travelling in the TARDIS," the Doctor noted, "So, why don't you tell us where you're from originally."
"My name is Lily Thomas," she introduced herself holding her mug tightly, "I work for UNIT."
"When?" Rory asked.
Lily shrugged, "It was 1973 when I was taken by that man."
"Do you know who the man was?" the Doctor asked.
Lily nodded.
"Who was he?" Rory asked getting a sharp glance from the Doctor.
"He called himself the Master," Lily shuddered, "Claimed he was a Time Lord, just like you, Doctor."
The Doctor nodded.
Lily took a deep breath, "He told me he wanted to perform a small experiment, to create a half-human child for something. He extracted my eggs then a few weeks later implanted them in me so I would carry the ones that were viable."
Rory looked at the Doctor visibly shaken.
"How many children did you have, Lily?" the Doctor asked.
Lily wiped her eyes, "Just one," she took in a shuddering breath, "What happens to my baby? Please tell me he is safe."
"Tell her," Rory pleaded.
The Doctor nodded softly, "Lily, your son was taken in by two wonderful people who raised him to be caring and compassionate. He became a nurse, met a girl he adored and married her."
Lily smiled holding back tears.
"And he's sitting at your side," the Doctor finished.
Lily spun to look at Rory who smiled at her, "Hi."
The Doctor left Rory and Lily to talk for as long as he could while he programmed the TARDIS to protect Rory's history. She had already done this but if he didn't give the instruction it would cause problems later on.
He checked the clock.
There was only a short time he could allow them to spend together before he had to separate them for their safety. Once that was done then he would study the files he'd stolen and discover exactly what the Master had done and what that meant for Rory.
Although he gave them every second he could the Doctor knew they had run out of time. He left the TARDIS finding mother and son hugging.
"I'm sorry," he interrupted them, "But Lily, it's time."
Taking a deep breath she pulled back and studied Rory's face for a moment, "I could never have imagined how wonderful you would turn out to be and I am so sorry I had to leave you. I will always love you, Rory. My son."
Rory smiled softly, "I love you too, Mum."
With a final embrace she walked into the TARDIS without looking back.
x
"Tell me something," Lily said as she leaned against the rail.
The Doctor looked over at his guest as he piloted the TARDIS back to UNIT in 1973, "If I can."
"Will you look after Rory?" she asked.
The Doctor smiled at her, "I have and will always look after him, Lily. I promise. He is my family."
She wiped her eyes and shuddered, "I was so scared. Alone and suddenly pregnant but then...oh then there he was so beautiful. I know I can never see him again but make sure he knows I want to. Make sure he knows that I will always love him."
The Doctor moved to her side and rested his hand on her arm, "He knows."
Without another word he opened the doors to the TARDIS and stepped out finding the welcoming committee waiting for them looking bemused.
"Brigadier," he greeted the man with a grin, "I don't have time to go over this. I'm sure you know Lily Thomas. She'll tell you what happened but unless I mention it first don't speak about anything she tells you to me. Or anyone else."
"Doctor?" the man asked confused.
"I can't stay," he stopped the other man from speaking, "Lily will explain everything."
Without giving anyone else a chance to say anything he jumped back into the TARDIS and headed back to check on Rory.
x
Rory sat watching the TARDIS disappear then reappear within two minutes knowing he'd never see his birthmother again, the same way he would never see the mother that raised him.
He'd told her his story, well a sanitised happier version without the random de-aging and multiple deaths.
"I've returned her to her own time," the Doctor said the moment he stepped out the blue box, "UNIT will look after her."
Rory looked up at him, "Thank you."
The Doctor nodded, "Now we have to investigate what your non-human side is."
"I don't think I want to know," Rory whispered.
"I understand," the Doctor told him, "But considering this was done by the Master then I need to know. I need to make sure I can keep my promise to the women who love you."
Rory stood and pushed a hand through his hair, "Tell me when you find it. I need to get some air."
The Doctor nodded and Rory headed out the office down the stairs then went for a walk around the University.
"Should I ask or should I just find something that will actually get you drunk?"
The Doctor looked up to find Nardole standing there watching him, "I'd take the drink but right now I need to be completely conscious."
Nardole frowned, "Is it that bad?"
"It's..." he hesitated, "Concerning. When he had no idea that he wasn't fully human Rory was safe but now he has the knowledge..."
"He can't leave," Nardole noted with a grimace.
The Doctor nodded, "The TARDIS is the safest place for him to be and I don't know if he'll accept that."
"Are you going to tell him what you found?"
"I'm not sure," the Doctor sighed, "I should but telling him is adding another alarm in his psyche and not telling him could push him away from the safest place there is."
Nardole sat down and leaned back in the chair, "She told me about him once."
"Who?"
Nardole rolled his eyes, "River Song, who else. She told me about her father one night, about how incredible he was. Do you want to know the one thing I took from the story?"
"What was that?"
"That he was her hero," Nardole said, "That her father was someone who would do what was best."
The Doctor smiled slightly, "Thank you, Nardole."
With a nod he stood and left the room once more before calling back, "I'll have tea ready for when you talk with him."
x
"How was your walk?"
Rory held up the bag he was carrying, "I picked up some more Jammie Dodgers," he said before taking his seat and a deep breath, "What did you find?"
"If I said that I can't tell you," the Doctor asked, "In order to protect you, would you accept that?"
Rory stared at him, his eyes showing that he was going over everything in his head. He finally looked up and asked, "If I said I want to know will you tell me?"
"Yes."
"Then I trust that you're keeping this from me for a very good reason," Rory told him.
The Doctor stared at him surprise clearly on his face.
Rory chuckled slightly at the other man, "You always focussed on Amy, Doctor. You forgot me sometimes and you still forget how much I pay attention. You do things to help the people you care about and I know, even if it took me some time to realise it, you do care about what happens to me."
The Doctor stood and walked around the room for a few moments before turning back to Rory.
"Just now the best thing I can do is keep this information from you," the Doctor told him, "I promise that as soon as I am able to I will tell you everything you need to know."
Rory nodded, "Thank you."
"You should be fine to resume a life here," the Doctor told him, "Find a job, go to the movies and whatever else you humans like to do."
Rory looked at him with a slight grimace, "Are you kicking me out?"
"Never," the Time Lord replied, "The TARDIS itself came for you, she chooses the people she wants to keep onboard and she has always liked you."
A slight smile touched Rory's lips, "Amy used to complain about that."
"So do I sometimes," the Doctor threw in.
"I think I'd like to stick around here for a while," Rory told him, "I have some money, Amy and I opened some savings accounts which I can access just in case we needed them. We were never sure if we would manage to find a way through time so wanted to be prepared."
The Doctor smiled and offered his hand, "Welcome home, Rory Williams."
Rory took the other man's hand shaking it feeling for the first time since he'd lost Amy he had a home again.