It was nearly seven on the third day when the Doctor finally woke from his lengthy slumber. He could feel the warm blankets and comfortable pillows, and glancing around, realized that he was lying in Amy and Rory's lounge. His Time Lord senses and the sight of the sun setting told him that it was about 6:15 in the evening. The Doctor was aware that he had awakening from a post Time Lord coma haze.
Amy walked in and stopped dead, "Doctor!" She rushed over and sat next to him. He leaned into her shoulder. "Welcome back, Raggedy Man. " She smiled.
"How long have I been-?" The Doctor croaked, but was interrupted by Amy hugging him.
"About three days," she interrupted with a giggle.
The Doctor sat up, "Three days?! I've been sleeping in your lounge for three days?"
" 'Fraid so," Amy replied with a casual shrug.
He put a hand to his head, "The last thing I remember is talking to the King and Queen..."
Amy's expression clouded, "You fainted, Raggedy Man, tore your stitches. How long were you in pain? Rory told me you kept injecting yourself with something."
"Pain killer," The Doctor replied, not looking at her. Until it didn't take the edge off anymore. I'm sorry that I worried you, Amy?"
"I'm just glad you're alright, Doctor." She kissed his brow.
He looked around, a little bewildered at the absence of his 'box'. "Where's the TARDIS?"
River took Jack back home or wherever. She should be back soon." Amy grinned, "C'mon, Rory went for Chinese take away. I'll call him and get extra portions."
Amy and Rory tucked their son into his new bed after practicing signing a bedtime story. The Doctor watched with a sad smile on his face. He hadn't schooled it fast enough as Amy caught it when she turned around.
"What's that face for, Doctor?" Amy inquired, frowning.
The Doctor put a finger to his lips and led the couple down the stairs and into the kitchen.
"Alright Doctor, what is this about?" She demanded, placing a hand on her hip.
The Doctor glanced down at the floor, "This isn't a done deal yet." He said in an undertone.
"What do you mean?" Rory asked patiently.
"We still have to talk to the Shadow Architect about you adopting an alien into your family, since it's never been done before." The Doctor explained. "She...really has the last word."
"I'll not have Alex taken from me, Doctor. Not after everything that has happened, even if I have to yell, kick and scream." Amy replied firmly.
The Doctor chuckled, "Well, I hope it doesn't come to that. I don't think that she'll win an argument against you."
The TARDIS returned nearly an hour later. The Doctor told River of their plan to speak to the Shadow Architect, and all the adults agreed that they would leave the next morning. Tension was thick the next day as they got up and readied themselves to face the Shadow Architect.
"I don't want to think about the 'what if's," Amy told Rory as they helped Alex into his shoes, "We can only hope that 'The Architect' whoever she is, will let us keep Alex.
When the TARDIS took off, The Doctor was looking around at his new control room with wonder and amusement.
River caught him tugging at his shirt collar. "Is she that intimidating, Doctor?" She teased.
"Well...we didn't leave one another on the best of terms. Remember when the Earth moved and all those other planets were in the sky?"
The couple shook their head but River nodded, "I remember."
"The Daleks were the cause of it. The Architect and I had a disagreement with what we each thought should be done. I needed to save my friends who were captured by the Daleks, and the Architect wanted to go to all out war with theme. Needless to say, we disagreed and I left to follow my own plan. "
"Doctor, not to change the subject, but..do you have a nickname...I mean, I know you can't tell us you're real name."
The Doctor's hazel eyes sparkled, "Theta. My tutors use to call me Theta." He replied dreamily, perhaps remembering a time long ago on Gallifrey.
"Doctor?" Amy interrupted his daydream, "How do we tell him about...his past?"
The Doctor placed his hands on her shoulders and smiled, "Just tell the truth, it's the best way."
The TARDIS finally reached its destination with a heavy thud that signified their arrival. The Doctor stepped out cautiously, followed by the others. They were greeted by a Judoon squad, all with rifles trained on them. Amy and Rory instinctively put their hands up.
"Space rhinos, that's a new one." Rory commented
"Not too strange since we've traveled with the Doctor," Amy returned between her teeth.
The leader of the Judoon squad stepped forward and began to speak in a rapid dialogue of strange words. The Doctor answered them in quick succession, and added something else.
"I will speak with The Doctor." A commanding feminine voice called out from behind the Judoon.
The rhino guard stepped out of the way to reveal a woman who looked like she belonged in the 18th century France, save for the deep crimson eyes.
"Is that-the Shadow Architect?" Amy asked quietly, and Rory just shrugged.
The Doctor nodded his head in greeting. "Architect, these are my companions, Amy and Rory Pond. And my wife, River Song."
"Williams!" Rory hissed the correction without looking up from his deep bow.
"And this-" The Doctor continued without noticing the amendment, "is their son, Alex. He was a citizen of the Sky Djinn."
The Architect's eyebrows rose as she glanced at the child.
The Doctor explained the story in its entirety, and she listened with silent deference.
At the end of his tale, the Shadow Architect nodded. "So the child was not offered a home on his own planet, and was unwanted by his people?"
"Alex would have been put in an orphanage and ostracized by his own people due to his loss both his powers and his senses." The Doctor acknowledged.
"With no one to protect him, the Prince would have killed him, or he would have died during a scourge in Earth's history." He bowed his head further.
"Your um...Majesty, we ask that Alex official become our son, that is, that we be allowed to adopt him." Amy blurted out, interrupting the Doctor's explaination.
The Architect looked from Amy to Rory, "And what makes you think that you can care for an alien child?" She posed the question to them with narrowed eyes.
"We've already bonded with him, and have taught and learned how to communicate with him. "
The Architect stepped forward and knelt to look at the boy. "Speak to him, ask if he wishes to stay with you." She ordered.
Amy bent, and posed the question to her son. Alex's eye dulled with worry. In a moment, Amy answered for him. "He says yes, he does want to stay, and is he going to be taken from us?"
"That has yet to be determined," The Architect said shortly, "Ask him if he wants to stay on Earth."
Amy again put forth the question and rapidly answered, "Yes, I like it."
"The next question is for you two. Will you care for him all of his life? And do so without telling anyone of his origins?"
"Yes, of course." Rory put in without hesitation. "We've been hoping for a child, and to rescue a boy who needed a home and a family-"
"That answer is enough." The Architect replied shortly.
"Please-" Amy imposed, "Please don't make us take him back. After everything that's happened to Alex, I want him to be happy."
The Architect straightened up, and looked at the little family, pondering for a minute. After this pause, she decreed, "Very well, I shall allow you to formally adopt the child."
There was a shout of glee from Amy that rang through the marbled hallways.
"What is his full name?" The Architect inquired without the same emotional tone.
Amy answered instantly, "Alexander Brian Theta-" This raised The Doctor's eyebrows, "Williams."
The Architect nodded, "Very well. I hereby relinquish all rights to you Rory and Amelia Williams, to raise the child Alexander Brian Theta Williams, child of the Sky Djinn."
Both she and Rory hugged Alex. "Thank you, thank you so much, m'am!" Rory exclaimed.
The Architect clapped her hands twice, and a Judoon appeared with a large scroll of paper and a quill pen. She signed the parchment at the bottom, then rolling it up, handed it to the couple.
"There are two stipulations to this arrangement." She announced with a booming tone, "One, you shall never again travel with the Doctor."
Amy looked solemnly at The Doctor, "We've...been thinking about stopping. Now that we have Alex, we really can't leave Earth. We agree to this."
"The second is for you, Doctor." The Architect spoke to him next, "Once you leave Earth, you may not visit these two again. "
"Wha-? But the Doctor is our family! We're not just going to forget that he exists!" Amy protested and stepped forward to challenge the other woman.
"He carries with him an ancient secret that can tear worlds apart. Danger seeks him everywhere he is present, and thus puts all who are around him in danger." Her steely glance went to The Doctor, who just looked away.
"I agree to this," The Doctor choked out, while a tear slid down his face.
"Doctor we can't just have you out of our lives just like that!" Amy insisted with anger.
"Mother," River consoled, placing a hand on her shoulder, "Please understand, he is doing this to protect you."
"But-he- we love him!" Amy spouted, with tears coming into her eyes.
"As do I, Amy. But now you have another to look after." The Doctor returned wisely, wiping away tears. "Thank you Shadow Architect." He turned to the woman and bowed, before they were shuffled back to the TARDIS.
The mood was very subdued when the family returned home.
"Why did you promise that, Doctor?" Amy finally burst out as they stepped out of the TARDIS. "We'll never see you again."
"To protect you, all of you." The Doctor admitted, without looking up at her, striding to them both and hugging them. "You deserve to be happy as well, Amy, Rory."
"So do you, Doctor." Amy said firmly.
"I will stay as long as possible," The Doctor husked through an strained voice, "If-if you'll have me, of course."
Amy kissed him on the forehead, "Of course, Doctor!" She laughed through tears, which gave the Doctor courage to smile. She tugged at Rory's arm, "C'mon, let's go phone my parents and yours and tell them about the adoption!"
"What, that we just adopted an alien child?" Rory spluttered.
She just rolled her eyes and pulled him into the sitting room.
When they were alone, The Doctor scooped up Alex, "You're already making your mum and dad so happy. I know that you'll grow up with all of their love." He kissed the boy's head, "As much as they have me."
The child looked up at him, perhaps intrigued by the Doctor's moving lips, because he laid his head on the Time Lord's shoulder and fell asleep.
A moment later, Rory came in holding a black cube in his hand. "Doctor, do you know where this weird box came from, by any chance?"
Much to everyone's surprise, The Doctor remained on earth for almost a year. It was due to what was dubbed "The Slow invasion". Eventually, he had rented a flat on the street opposite the Ponds, while River, with the help of the Vortex Manipulator, returned to her work as a archaeologist. At first, not traveling had driven The Doctor crazy, finding things to do to fill the hours of the day. But at last, he began to settle. Holidays, anniversaries and birthdays were celebrated. Amy and Rory decided on a date for Alex's would be November 23rd.
The mystery of the numerous black boxes all around the world that appeared out of nowhere didn't seem like it was ever to be solved, until the day when they came to 'life', so to speak.
The Doctor had taken comfort in the discovery of Kate Stewart, daughter of his beloved friend the Brigadier, had taken over U.N.I.T. But it had been she and River (who he had called to take on the instigator of this strange invasion, while the Doctor communicated with her on in a U.N.I.T. control panel. The damaged had been done however, many had simply collapsed or died from cardiac arrests. Those who were still alive were being aided in recovering from their ordeal. In time, what had happened was put out of the minds of Earth's inhabitants, though there was no explanation as to what exactly had happened, though a cover story was fabricated.
Nearly a month later, The Doctor, River, and the Ponds were playing virtual tennis on the Wii system, when the outer telephone of the T.A.R.D.I.S. rang. The Doctor turned, and spoke to Rory while pointing to it. "That's not suppose to happen." he muttered. Jumping the couch, he raced over to the faux telephone box and answer it.
"Hello?" He looked genuinely surprised at the outer telephone ringing, and pointing at it with a grin. "What's that? An invisible monster walking around your castle? The 32nd century? Earth's Moon? Right...right. We'll be there soon!" The Doctor smiled broadly at River, "Ready for some adventure?"
River's expression mirrored her husband's, "For you sweetie, always."
He grabbed her wrist and began to rush through the doors, when he heard Amy behind him. "Doctor!"
The Doctor turned to see Amy's eyes shimmering for tears.
His smile diapered as he took her in his arms and hugged her and Rory tightly for a few minutes.
Amy sniffled as she tried to smile. "Take off, Doctor. Go...save the universe." She spoke to River next to him, "River, you be a good girl and take care of him."
"I will," She winked at her Time Lord husband, and chuckled.
Amy stood on tiptoes to kiss the Doctor on his forehead. "Raggedy Man," she said between sobs, "...goodbye!"
The TARDIS de-materialized a few seconds later, with both Time Lord and Time Lady at the helm of the control panel. The Doctor wiped away stray tears and sniffled loudly.
River put a hand on his shoulder and kissed his cheek. "They'll be fine, Doctor. Amy and Rory are together, and they have Alex."
"No they won't..." The Doctor husked. Then turning to his wife, he beamed, "They'll be amazing."
THE END.
A/N: Thank you for sticking with me and for reading watching and faving this story. I hope that you enjoyed reading it as much as I did writing it.