The Doctor now sat on the floor of the TARDIS, attempting to read. His younger self was supposed to have "rest time" in his room. He knew being Gallifreyan meant the child wouldn't sleep much. Still, the Doctor implemented the daily ritual when he found himself snapping at the boy for asking incessant questions about any and everything.
Usually, the Doctor loved to put his intelligence on display, but after three years of feeling like he was being interrogated like he was some kind of terrorist, he needed a break. Thus, "rest time" was established. John was required to stay in his room and play with toys or read independently. Just as long as he allowed some time for his little mind to calm down.
The Doctor turned a page in the worn book. John always left his books around. He developed the habit of reading multiple books simultaneously and never actually finishing them. When The Doctor questioned John about it, he simply said, "I don't like endings." The phrase stung the older man's hearts. He knew the boy just meant it in regards to the stories, but the Doctor couldn't help but wonder if some of his actual memories or feelings were starting to bleed into John's subconscious.
He turned the page of John's most recent literature, "The Prince and the Pauper." All of a sudden, the TARDIS phone rang.
"Yes? What? I'm trying to read." He said with an unamused tone.
"Miss Clara and her concerns about the snow." Said the familiar voice. It was Vastra. Apparently, John's cheeky "friend" was not going to give up.
"I gave her the one-word test."
The Doctor rolled his eyes. "That's always pointless. What did she say?"
His curiosity got the better of him. "Well?...well?"
"Pond."
…
The Doctor told John to stay in the TARDIS while he went on an "errand." John knew that meant he would go have an adventure without him.
"So, I've set the parameters of the TARDIS so the alarm will go off if you leave," said the Doctor.
"Please don't make me stay here!" John begged.
The Doctor thought it over. Maybe if he gave John a bit more freedom, the boy wouldn't feel like he had to lie about where he snuck off to.
"Fine," said the Doctor.
John immediately brought the Doctor into a tight hug around his legs.
"Thank you, thank you, thank you!" He said.
John now sat next to Strax at the front of the carriage. The Doctor insisted that he needed to do this part on his own. So, dressed as Sherlock Holmes, he'd gone into the house of The G. I. institute. John obeyed, knowing not to press his luck. He was just happy to be tagging along.
"I'm bored," complained John. Strax looked at the child with an annoyed expression.
"Can I see your gun?" he asked with a hopeful face.
"Absolutely not, boy. I wouldn't even let the other one touch it. Certain he would end up shooting me. Who knows what you would do with it," Strax huffed.
John sighed and put his elbows to his knees as he cupped his face in his hands.
Suddenly, The Doctor came barreling out of a window straight for the carriage. He jumped inside and yelled at Strax to drive. He gave the Sontaran play by play directions of where to go. They ended up on the street in front of a large home. The Doctor popped out of the carriage back in his top hat and usual Victorian clothing.
"Now, you two stay here. I need to have a look at something." With that, The Doctor once again left the two to wait patiently while he "had all the fun."
Strax's communicator began to beep.
"Madame?" he answered. "Yes. Yes. I see. Of course." He then hung up.
"Madame Vastra wants me to see if The Doctor needs help with his investigation." He said to the boy.
John hopped down from the carriage and started walking in the Doctor's direction.
"Where do you think you're going? YOU are supposed to stay here." Yelled Strax as John began walking quickly away.
"I'm…just going to have a look at something." He said with a wry smile, echoing The Doctor's own words.
Seeing that the boy would not listen to him, Strax reluctantly hopped down and followed him. He figured that he may as well keep track of the child as not to anger the Doctor too much…he hoped.
John found the Doctor muttering to himself while looking over what appeared to be a frozen pond. The Doctor turned when he heard someone coming up behind him. He immediately frowned when he saw John and then Strax straggling behind.
"What are you doing here?" He questioned. Strax caught up with John and spoke.
"Madame Vastra wondered if you were needing any grenades?"
"Grenades?" questioned The Doctor. John was giggling.
"She might have said help." Strax quickly added.
"Help for what?"
"Your investigation!" Said John excitedly.
Seeing as now the two were not going to leave, the Doctor sighed.
"Who says I'm investigating? Do you think I'm going to start investigating just because some bird smiles at me? Who do you think I am?"
"Sherlock Holmes," said Strax. John could sense that the comment was pressing the Doctor's buttons and intently watched the two argue. He couldn't help laughing when The Doctor called Strax a "potato."
"Now go away," the Time Lord said, gesturing to both John and Strax. Strax obliged but not after calling the Doctor "Holmes" one more time. John, on the other hand, was not about to leave now that things were finally getting interesting. Before the Doctor could convince the boy otherwise, a light came through a window as Clara peered out. She waved at them, to which they both waved back awkwardly. Then she gestured for them to come in.
The Doctor quickly turned around, seeing John smiling up at Clara still waving.
"We're leaving. We're not going up. Leaving." He was muttering to himself, making John laugh at how flustered he was.
The Doctor turned around and then gestured to Clara that he'd be up in five minutes for some unknown reason. The Doctor looked at his own hand in shock.
"I thought you said we were leaving?" Questioned John.
The Doctor sighed as the two began to walk away from the pond.
John was quietly following behind The Doctor as they went to the front door.
"It's locked," said John as he tried to open the door.
"Well, obviously, it locked. It's the middle of the night!" Said The Doctor in a bit harsher tone than he'd meant to. The boy seemed to fold in on himself. He really wanted to show the Doctor he was clever so he'd let him come along on more adventures. John felt like he was already ruining it.
"I'm sorry," he said softly.
The Doctor closed his eyes and sighed.
"No. John. I'm sorry. Sometimes I can be a bit thick. You really are very bright. And clever." He added with a smile.
John had a wide grin. The Doctor took out his sonic and unlocked the door. John followed behind as they entered the dark house. They made their way up the stairs to try and find which room Clara was in.
Wandering into a dark room, John's eyes immediately went to the puppet stage. He ran over to look at it while the Doctor scanned the room.
"Doctor, look! Puppets! I've read about these in books!" John giggled as he picked up the "Punch" puppet, got behind the stage, and began making silly voices. The Doctor's hearts pricked again, realising John had never seen a simple puppet before. All of a sudden, there was a loud commotion accompanied by screams.
The Doctor quickly ran behind the stage with John to hide, not knowing what was coming through the door.
Soon Clara and two small children burst through. They seemed to panic as a scary ice woman broke through the doors. John immediately clutched onto the Doctor and pinched his eyes shut. Seeing how terrified John was, the Doctor took the puppet just as the small boy began to ask where "The Doctor" was.
John reluctantly opened his eyes in time to see the Doctor give him a smile as he began to talk in a silly voice with the puppet, asking, "Doctor? Doctor? Doctor who?" He then whipped out the sonic and aimed it at the ice woman, melting her.
John giggled as the Doctor continued to be silly by making the puppet kiss him. They both came from out behind the stage.
John waved shyly to the children as the Doctor looked over the soaked carpet.
…
John currently found himself sitting on a sofa with Francesca and Digby. He was thinking about when the Doctor was going on about the ice and what was happening. John was in awe of the Doctor. He'd never seen him behave with so much enthusiasm as he was usually somewhat grumpy.
John was aware that something terrible had happened to the Doctor to make him want to give up his adventures. It put a smile on his face to see the Doctor in action. He was disappointed that he was supposed to stay in the study and not help, but at the same time, he was relieved. The ice lady scared him quite a bit. Not that he'd ever admitted it.
It was a new experience for John to be in the company of other children. He didn't have much experience with his own age group. He was either in the TARDIS or with the Paternoster Gang. And in the evenings, he was usually with Clara at the Rose and Crown whenever she had a shift, and there were never any children there.
"You're very quiet," said the girl. "Not like your father."
John weakly smiled at the thought of the Doctor being his father.
Suddenly, a loud "whumph!" noise came from outside.
"What was that?" asked Vastra.
"It's Clara," said Jenny.
Hearing Clara's name, John sprang up and ran to the window. The adults were all talking, but John wasn't paying attention to what they were saying. Instead, his eyes locked onto Clara's body. Lying in the snow. It appeared she'd fallen from somewhere, and John instinctively knew wherefrom as the tears already started to form in his eyes.
He then heard Vastra say, "she's dead."
It was as if the whole world had stopped. John didn't know what to do. He heard the TARDIS materialising, and moments later, the Doctor was carrying Clara's body out into the study and lying her on a table. John immediately went over to her as the Doctor went back into the TARDIS.
Strax scanned Clara's broken body with an advanced medical device while John watched her intently. He was whispering softly to himself, "please wake up. Please wake up."
Clara had been the only person in his life who didn't treat him like he didn't belong. Yes, he had the Doctor. But he was cold and distant. John had memories of when the Doctor took the time to teach him how to read, but once John could do it himself, it was like the Doctor was done with him and was only there to keep him locked up.
Vastra was also cold and distant with him, much like the Doctor, if not worse, being she had different views on how children should behave. Then there was Jenny. She was the closest thing he had to a mother. She'd spend time with him teaching him how to make tea and biscuits, but she and Vastra were always so busy with their investigations that they barely noticed when he'd sneak out of his room on the nights the Doctor allowed him to have a sleepover.
And then Strax. Well, Strax was Strax.
Clara seemed to genuinely want to get to know him and cared about what was going on in his head. Even if it was a bit disorganised and random. She'd laugh at him, but he could tell she wasn't being cruel like most other people he encountered. He didn't know much about love, but he did know he felt it whenever he was with her. She didn't just care about his wellbeing but about who he was as a person. Even in his child-like mind, John could tell the difference between when someone was being genuine or not.
The Doctor came out of the TARDIS and put his hand on John's shoulder. John looked up at him and understood that the Doctor wanted a moment with Clara. John reluctantly stood up and moved away. He went over to the window, looking out into the snow where Clara's body had been lying moments before and began to cry.
…
The Doctor left with Vastra in the TARDIS to take care of The Great Intelligence.
John went right back to Clara's side. He watched as she slipped in and out of consciousness.
"Your father is a good man, John," said Clara as she closed her eyes in pain.
John couldn't help the tears flow down his cheeks.
"Hey, hey," she said soothingly. "It's going to be okay."
John had his head down as he rested near Clara. His head shot up as he heard the TARDIS materialise in the room once again. The Doctor and Vastra stepped out.
"I'm sorry. There was nothing to be done. She has moments only," said Strax as the Doctor slowly approached Clara. He knelt down on the opposite side of where John was. The boy was softly crying as he watched the Doctor talk to Clara in her last moments. He heard The Doctor say he wouldn't go back to his cloud. Then Clara said something strange just before the clock chimed out for midnight as she passed away.
...
Standing beside the Doctor while they waited for the Latimer's to say goodbye, John felt oddly numb. The Doctor and the other two women were quietly conversing, but he didn't pay attention. John followed as the Doctor made his way over to Clara's gravestone. It had been a fortnight since she'd passed, and they'd already gotten her a headstone. John knelt down next to the Doctor. He'd never known anyone die before, let alone even been in a graveyard. He probably would have been a bit scared had he not been so sad.
The Doctor read Clara's name as something occurred to him. "I never knew her name. Her full name."
John looked to the Doctor and saw the puzzled look on his face as he started rambling something about souffle and how he'd met her before with the Daleks (whatever those were).
"Doctor?" called Jenny. She was confused as well.
"The same woman, twice. And she died both times. The same woman!"
The Doctor was on his feet, now seemingly getting riled up. It scared John a bit because he didn't understand what was happening.
Now they were all confused.
"Doctor, please, what are you talking about?" asked Vastra.
John stood behind the Doctor as he continued to explain without actually explaining anything.
"Right, you two stay here. Stay right here. Don't move an inch!" Said the crazy Time Lord to the two women, completely ignoring John.
"Are you coming back?" yelled Vastra as the Doctor ran off. John looked to the women then to the Doctor before running as well. The Doctor didn't tell him to stay put, so why should he?
The Doctor was fast, but so was John. He'd caught up with the Doctor in no time just as he entered the TARDIS. John followed right behind him as the Doctor began flipping around the console. Just as he threw the lever, the Doctor looked up and saw John staring at him with eyes wide.
"John!" exclaimed the Doctor. He was so focused on the impossibility of Clara Oswin Oswald that he completely forgot about the 5-year-old boy standing now a few feet away from him.
"Doctor, what's going on?" John questioned.
The Doctor's first instinct was to take John right back to the Paternoster Gang but seeing the terror mixed with pure excitement and curiosity in his face melted his hearts a bit. So, instead, he smiled at the boy as he spoke.
"We're going on an adventure."
...
The Doctor sat on a swing and watched John playing on the modern playset. His "mini-me" laughed as he climbed up the apparatus and slid down the metal slide headfirst. The elder Time Lord began to think he'd never find Clara again while John was getting restless. So he figured a quick stop to stretch their legs and get John's boundless energy out wouldn't hurt.
A little girl took the swing next to him. "Hello." She said politely.
"Hello."
"Why are you sitting on a swing?"
"Why shouldn't I?"
"Because you're old," said the girl with a matter of fact tone.
"Yes," he chuckled. "That's true. That is very true."
John caught sight of the little girl talking to the Doctor and slid down the slide one more time before making his way to the swings.
"Hello!" Said John happily.
"Hello." Said the girl. John smiled. "Can I swing with you?" The little girl nodded, and the Doctor hopped off the swing to let John have a turn. The girl looked over at the funny man.
"Are you his father?" She asked innocently. They both responded at the same time. John saying 'yes' and the Doctor saying 'no.'
John quieted and hung his head down. The little girl grew uncomfortable at the tension that was forming. The Doctor noticed.
"Hey, is that your mum?" He nodded over towards the woman watching them.
"Yeah, I'd better go and see if she's all right."
"Yeah, I think you better had."
The little girl hopped off the swing and waved to John.
"Goodbye." She said. John just made gave an incoherent sound.
"Goodbye." Said the Doctor as the little girl skipped off towards her mother.
The Doctor could tell that John was trying not to cry, so he knelt down beside him. He hated this part. He tried to explain to John multiple times that he was not his father, but John kept getting confused as he read more literature about children who often had families. John would often call him "dadda" when he first learned to speak. The Doctor assumed he was just trying to say "Doctor", but maybe he was really trying to say "daddy".
"John, you know I'm not your father. It's complicated, and I know it's hard to understand, but I promise you one day you will."
John wiped at his silent tears as they made their way back to the TARDIS.
John stepped inside as the Doctor followed behind him.
"John?" questioned the Doctor. John slowly turned, tears still streaming down his face.
"You don't want me." He said, sniffling.
The Doctor was caught off guard by the emotion and hesitated. John took the silence as confirmation of his statement as more tears fell. He turned and ran to his room.
"John! Wait. I...I didn't mean…." The Doctor chased after the boy and came to his room, where the door was firmly closed. The Doctor approached the door and softly knocked.
"Go away." Yelled John, clearly hurt.
The Doctor considered ignoring the boy's wishes and opening the door with his sonic. Instead, he went for the handle and hesitated. His hand dropped to his side before he made his way back to the console room. He went straight to his view screen and began to sift through more information about Clara.
The tweed-wearing alien was having a hard time thinking clearly. His emotions were all over the place. Part of him wanted to go to John and make things right, but another part of him was so enthralled by the mystery of Clara Oswald that it consumed him.
He needed to find a place where he could quiet his thoughts. The Doctor punched in some coordinates and made his way to 13th century Cumbria.
…
John was running through the poorly lit corridors of the monastery, trying to hide from an angry monk. Over the past 6 years of living in such a dreary environment, John developed the habit of "pulling pranks" on the younger monks. He was eleven years old now. Bored didn't even begin to describe his angst towards leaving this place. The Doctor spent most of his time locked in his room doing who knows what. That left John on his own to wreak havoc on the very religious and unsuspecting men of the monastery.
"John!" the boy heard his name being called. "I swear if I find you, I'm going to…well, I'm going to tell the Abbot!" exclaimed the young monk.
John snickered to himself, hearing how flustered the young man was. He had to entertain himself somehow, and if that meant adding a "special ingredient" to the monks' disgusting stew, so be it. And by "special ingredient", spiders and insects seemed to be John's preference. An occasional toad would do if he happened to stumble upon one during his unsupervised wanderings.
The Doctor didn't seem like he was too keen on spending much time with John anymore. The first couple of years in the monastery, the Doctor still gave him lessons, but once John started asking questions like "why my willy is getting hard?" or "why does it feel good to touch myself?" the Doctor would just ramble on and then change the subject. And now, he seemed to be avoiding John altogether. The young Time Lord didn't understand why it was such a big deal or why the Doctor got so flustered with his most recent inquiries.
John made his way down the stone pathway through the dark halls towards the Doctor's room. When he reached the door, the Abbot and another Monk were already at the entrance.
'Shit,' he thought. (John had managed to sneak a few modern books off the TARDIS when they first came to the Abby. Unfortunately, the graphic novels were far from educational. He'd picked up a few terms that he didn't dare use in front of the monks, let alone the Doctor.
John quickly tucked himself around a corner and peered around to see what was happening.
He assumed the monks were there to punish him. The young boy stood off to the side as they entered the Doctor's room, muttering something about his "madness." Suddenly, he heard the Doctor scramble out of the room. John quietly followed the three men.
When the Doctor asked for a horse, John made his presence known.
"Where are you going?" He demanded.
The Doctor was mounting the horse as he spoke.
"The TARDIS. Hop on."
John was surprised that the Doctor was allowing him to come. On the other hand, the Doctor was in too much of a hurry to argue and figured bringing John along would be easier. John hopped onto the horse and wrapped his arms around the Doctor's waist as they rode towards the cavern.
They approached the TARDIS where the phone was ringing.
"That is not supposed to happen," said the Doctor as he reluctantly answered the phone.
John figured he may as well make the best of it, and he approached to enter the TARDIS. The Doctor was flailing his arms and mouthing at him to stay out. Still, he was slightly distracted at the odd conversation with someone about the 'internet' and eventually ignored John.
Seeing the Doctor would not stop him, John stepped through the familiar threshold. His face lit up as he ran his hands along the Old Girl's railing. He'd nearly forgotten what the console looked like. It was odd to think that he now spent more than half his life in the monastery than he had in the TARDIS. His eyes caught onto the sight of the Doctor's psychic paper sitting on the console. John picked it up and pocketed it.
The Doctor may have chosen to lean into the monk look, but John modelled his outward appearance after the people in his comics. He chose a white t-shirt and blue jeans with simple trainers.
John jumped when the Doctor burst into the TARDIS and immediately began punching in coordinates and flipping switches.
"Are we leaving?" Questioned John. The Doctor's head popped up as if he genuinely noticed John's presence for the first time that day.
"Ah. Yes. We are. Something has come up. I…I need to take care of something. I'm going to drop you off with Vastra for a bit, then come and get you."
Before John could protest, the Doctor picked up his mobile and called Vastra. John figured it was better than being left behind with the boring monks, so he let it go. His relationship with the Doctor was strained enough as it was. And maybe now that he was older, Strax would let him test out some of his weapons!
The Doctor pulled the lever in a rush and snapped his fingers as he shoved John out the doors. "Be back in a mo!" he said as she shut the doors in John's face.
John turned around as he watched the TARDIS dematerialise before his eyes. The boy looked around to take in his surroundings.
"Okay," he said quietly to himself. "This is new."