Chapter 50

There were obvious repercussions to Sherlock killing Charles Augustus Magnussen and everyday he told himself that what he did was necessary – it was the only way he could justify murder, but even some days that didn't make any sense to him at all. Killing him was the cowardly way out, and it didn't help that some nights that was all he saw when he closed his eyes. The moments afterward were a blur with Sherlock taken into custody, and John and Mary having limited visiting privileges. Mycroft successfully silenced the matter, and no newspaper, tabloid, or website would ever hear of what happened that night. Charles Augustus Magnussen died from a heart attack in his home at Appledore.

In true British fashion, Sherlock was sentenced a death penalty in the politest way possible: by disguising it as a mission. Only the mission never came to fruition when every screen in London began showing Moriarty's face. They needed Sherlock's help once more. He was back in the game, much to his dismay and utter delight.

This led to Sherlock waiting. And waiting. And still, waiting. After the broadcast, there was radio silence, but it still shocked the nation, and a minor panic ensued through some Londoners. Honestly, it was waiting for information that was the torturous part of Sherlock's day. Though a part of him cared that Moriarty was "back," another part cared more with the "how."

Sherlock was resolved to leaving time travel, and everything that went with it, all behind – he really was. He was fine with never seeing the Doctor ever again. His life returned to focusing on solving cases, not seeing the stars. With Amy gone, and Mary and John back together, life could return to some form of normality. But oh, how he wished that the Doctor were here to bring him just a few days or weeks into the future so that he needn't wait any longer for a call from Mycroft.

"Lestrade called, said you're not answering his texts?" John popped his head into the kitchen of 221b.

"I'm busy and he doesn't have any information for me on Moriarty," Sherlock, working on a side project, kept his eyes on the Bunsen burner – he thought that a distraction might help (it didn't).

"I think it's a case," John shrugged, taking off his jacket and walked towards the living room, intending to place his jacket on his chair. "If you aren't busy with this Moriarty business."

The sound of electricity crackling in the living room usually wouldn't alarm John – he'd think it was Sherlock doing another one of his experiments – but the odd, abrupt, and ear piercing sound and sudden wind inside the flat put John on high alert. Sherlock knew what was happening but immediately recognized that something was extremely wrong, and he jumped up from the table and pulled John back into the kitchen. They both watched, Sherlock confused and John horrified, as the TARDIS crashed into, and effectively demolishing, the desk, taking a part of the bookcase and mantle with it, and then dangerously tipping on its side. Luckily the TARDIS managed to stand upright, crashing down with a loud thump echoing throughout the living room. The cloister bell rang on and on.

Just a few moments before …

"Kidneys! I've got new kidneys!" the new Doctor grimaced. "I don't like the colour."

"Of your kidneys?" a frazzled Clara asked.

The TARDIS, under no control of either party, began to shake and wobble dangerously.

"What's happening?"

"We're probably crashing!" the Doctor fiddled with the controls.

"Into what?!" Clara tried to hold on tightly.

"Stay calm. Just one question," the Doctor looked at her. "Do you happen to know how to fly this thing?"

Clara looked at him, shocked and her face forming anxious lines, before replying in a high-strung voice, "a little."

"Good, it's up to you now," the Doctor stood to one side. "Now I think I need to talk to a doctor about the colour of my kidneys. Oh! I know one … never met him, though."

Clara, bewildered as she was, was trying to remember anything the old Doctor taught her about flying the TARDIS, "What?!"

"Yes, yes, a name, I need a name. I know him from stories but who told me about these stories?" the Doctor stood uncomfortably close to Clara, his face just inches away from hers. "The man who told me stories. Who is the man that told me these stories of the doctor? The war doctor."

"I have no idea what you're talking about. Can you please help me?" Clara was basically yelling.

"No! His name! The storyteller. We need to go to him," the Doctor waved his fingers in front of Clara's face.

"To who?" Clara tried twisting and jabbing some buttons.

"Sherlock Holmes. 221b Baker Street, London," the Doctor rattled off this information like a robot, as if the info was engrained in his memory.

Just mere seconds later, the Doctor collapsed.

Currently …

Poor Sherlock Holmes and John Watson being completely blindsided at 221b. It was a good thing that Mrs. Hudson was out for the day.

"What in the bloody hell?" John stood stock still in the safety of the kitchen, but then noticed Sherlock approaching the big blue box. "Sherlock! Don't!"

Sherlock made his quick deductions, noticing first the obvious smoke coming out of the shattered glass windows. He knew there was someone inside the time machine, but his deductions told him that the box would have landed a little more smoothly if the Doctor was piloting – this only meant that someone else was controlling the TARDIS.

Suddenly, the TARDIS doors swung open and a billowing cloud of smoke engulfed the flat. Coughing, John went to the windows and opened them, covering his mouth at the same time. Sherlock had to reel back and he accidentally bumped into John.

"What is happening?" John asked, his eyes glued to the box.

A coughing girl came stumbling out before Sherlock could answer. Sherlock hurriedly went through his mental archive of companions, aliens, and other known associates of the Doctor, but there was no match. He did recognize her, though, as the bookshop girl in New York City.

"What the hell are you doing here?" Sherlock muttered.

She looked at Sherlock, but there was no sense of recognition in her eyes. She stood at a reasonable distance away from them, but she stuck close enough to the TARDIS doors to tell Sherlock that she was attached to the box in some way. She looked between the both of them, but chose Sherlock to direct her question.

"Are you Sherlock Holmes?" Her British accent told her that it definitely wasn't the girl in the bookstore – she was too panicked to fake one, and this one sounded authentic.

"Yes," Sherlock narrowed his eyes.

Twin? Unlikely. Same height, same features … clone? A little more probable.

"Good," the woman interrupted Sherlock's train of deductions and managed to grab a hold of his hand.

With surprising strength she dragged Sherlock into the smoking box and towards the console where Sherlock noticed a man laying unconscious on the floor. Things inside the TARDIS were in disarray, with lights blinking rapidly and emergency sounds going off, but that wasn't where Sherlock's attention was directed.

"He said you could help him," the woman kneeled down beside the man, supporting his head, but looked up at Sherlock.

"Who?" Sherlock remained in his spot, not quite sure who he was looking at.

"He said you know him," Clara looked at him, puzzled.

"I have never seen him before in my life," Sherlock tilted his head slightly, also confused.

"Yes, you must have. This is the Doctor, and he needs your help," the woman said so with such sincerity and desperation that it must have been true.

Something on the console unexpectedly exploded, startling the both of them.

Sherlock looked back at the entrance of the TARDIS where the smoke started to dissipate and saw John standing there, his face turning pale at what he could see, "we need to get him out of the TARDIS. This box is going to kill all of us if we don't. John!"

John's attention snapped back into reality, "Sherlock? What is …?"

"No time, get in here and help me," Sherlock ordered.

John visibly gulped and clenched his fists, taking the step he needed to get inside the time machine. John walked quickly to the group, but not before taking a look around.

"It's … bigger on the inside!" John exclaimed.

"Yes, yes, we have other matters to attend to," Sherlock directed John's attention to the apparent Doctor. "We need to take him out of here. Take his legs."

Sherlock hooked his arms under the Doctor and John lifted his legs. They carefully brought the Doctor into 221b and set him down on Sherlock's bed. Clara hovered the entire time to make sure he was okay. There wasn't much any of them could do, though. John, under a certain amount of shock after hearing the phrase "check both his hearts", managed to conclude that the Doctor's two hearts were beating and that he probably just needed rest – it wasn't like any of them really understood what regeneration was, how it worked, or how to deal with it.

They all found themselves standing in the living room staring at the broken table and bookcase amongst the other rubble. Oddly enough, it was through rubble and destruction that he met Amy, a former companion of the Doctor. Now, assessing the situation at hand, Sherlock supposed this would be the second time he'd meet another companion through rubble and destruction. Sherlock broke the deafening silence and that odd train of thought.

"Who are you?" Sherlock turned his head slightly to look at the woman.

Her demeanour and breathing had calmed down since the sudden appearance of the box, "my name's Clara. Oswald."

"And that man?"

She looked at him, puzzled, "it's the Doctor."

"No, it's not. The Doctor I know is not an elderly man," Sherlock corrected. "They don't even have the same bone structure."

"The Doctor you know, you knew, he changed. He got old and he changed his face. It's what they do, apparently. They change their face when they die," Clara tried to explain this to Sherlock, taking her phone out instead and showed him a picture of the Doctor he knew. "This is the one you know, right?"

Sherlock nodded, then wondered vaguely why the Doctor never explained this to him in the time that they spent travelling together, but the sound of his bedroom door opened prevented him from asking. The man – the Doctor – stood in the doorframe. John, Sherlock, and Clara slowly walked towards him, but the Doctor thought otherwise, grabbing John's shoulders hurriedly.

"You, you're the war doctor! Help me fix my kidneys!" the Doctor spoke in his thick Scottish accent before collapsing onto the floor, unconscious.

"For God's sake," Sherlock knelt down and dragged his body back to his bed, laying the Doctor down with a loud thump.

Sherlock returned to the living room to see Clara Oswald sitting on the couch looking worried, and John standing in the middle staring at the box.

"Will someone please explain to me what's going on?" John managed to break out of the spell.

"Tea?" Sherlock ignored the question and posited another question.

"Please," Clara spoke silently.

In the time between getting tea ready, Clara remained sitting on the couch, occasionally looking at Sherlock's bedroom door, while John migrated to his seat. Sherlock readjusted his chair from behind the TARDIS and sat down, taking a long slurp to break the silence.

"Okay, Sherlock," John began calmly, but began to yell. "What the hell is that?!"

Sherlock sighed, "It's a TARDIS. It stands for Time and Relative Dimensions in Space. It's a time machine that travels through universes and galaxies. That girl over there," Sherlock pointed to her. "Is one of the Doctor's companions. The Doctor is the man currently unconscious in my bed. He's an alien of whose age I cannot recall, but seems closer to 2000 years. Amy and Rory were once companions of the Doctor and they use to travel in space and time with him, saving people, defeating aliens, and the like. When I said that Amy was accustomed to dangerous situations, I meant it relating to this. Have I covered it all?"

"I ... w-what?" John stuttered.

"How do you know all of this?" Clara piped up, putting her mug down. "How do you know the Doctor?"

"I travelled with him once or twice. Learned a thing or two…," Sherlock continued to look at John. "About alien technology."

John abruptly stood up, his tea sloshing onto the ground, "I need to … excuse me, um, Clara."

John immediately walked out of the room.

"It's a lot to take in," Sherlock spoke.

"Yeah," Clara sighed.

And then John came back just as suddenly, "Amy and Rory?"

"They travelled through space and time with the Doctor. Then they got stuck in New York in the 1930s."

"Stuck?"

"As in they can't come back to the 21st century," Sherlock's voice went quieter. "They died in their 80's, sometime at the latter part of the 20th century."

"You can't be serious," John harshly laughed.

"Take a look around you, John. A box that is bigger on the inside magically appears in our living room, with an alien and human in tow. Why would I joke? Would you like more proof?" Sherlock stood up.

John stood there silently for a moment, "how long did you know?"

"About?"

"All of this. Bloody time travel, this Doctor, and Amy and Rory," John looked at Sherlock earnestly, desperate for answers that didn't sound so ridiculous as the ones Sherlock was spewing out.

"Since my fake suicide. While you two were on your way to St. Bart's, a future version of her, one that had already seen me fall, found me on that roof and told me who she was," Sherlock explained as succinctly as possible. "She wasn't able to tell me everything, just the very basics."

John looked down a moment, and then back up at Sherlock, "why didn't she tell me anything?"

"If she had told you earlier, it might've ruined any semblance of friendship. Would you look at her the same? John, you have to understand, she was waiting for the right time. It was circumstance of me possibly dying that brought it out of her sooner than she wanted," Sherlock tried to explain. "When she saw the Doctor die, not this one in my room but another version, she wanted to leave that life behind. It was too painful for her to talk about. Do you ever talk about the war?"

"No," John swallowed, his fists clenching.

"Her memories with the Doctor, all the good ones and the bad ones, were her own personal war she sought to forget when she watched him die, and my forcing it out of her through my fake suicide was the only way for her to tell me who she was. If I didn't, if St. Bart's and Moriarty never happened, I promise you there would have been a time where she would have sat us both down to explain," Sherlock walked over to the undamaged bookshelf and reached for the box on the highest shelf. "Everything you need to know about Amy is in here."

"What is this?" John reached out for it.

"Go upstairs, sit down, and just look through it," Sherlock said softly. "I think you'll understand better."

John looked at Sherlock for a moment before nodding, and then took his leave out of 221b. Sherlock returned to his seat and curiously looked at Clara. She had been watching that exchange with inquisitive eyes.

"Do you have siblings? A twin, maybe?" Sherlock asked once he knew John was out of the room – he wasn't sure John could handle this next part.

"No, but let me guess. You saw a girl who looked exactly like me?" Clara got the upper hand. "It was me. Not me, per se, but it was me."

"Explain."

"The Doctor, the past one, was dying. I jumped into his time stream to save him, and when I did that, I broke into a million pieces, and those pieces scattered through time and space with the one goal of finding the Doctor and saving him. That girl you saw is just an echo of me. Somewhere in her subconscious she'll want to find the Doctor and save him."

"I fear she may already have," Sherlock mumbled to himself, but changed the subject when he understood. "Why are you here with the Doctor?"

"Don't look at me. It's his idea," Clara looked at Sherlock's door. "He said that he didn't like the colour of his kidneys and that he wanted to meet a war doctor that could change it for him."

Sherlock blinked a few times, trying to register the ridiculousness of that statement.

"I know," Clara clasped her mug tightly, trying to make light of the situation. "Tell me about it."

"So what now?" Sherlock asked slowly.

"I don't know," Clara put her mug down. "I don't understand where to go from here."

"He's the same man, correct? Regenerated? Renewed?"

"I don't know. He's different. He's not like the old one," Clara shook her head. "He doesn't look renewed. Why does he have lines on his face? It's new."

"He looks different. He's older. Scottish sounding, but you're the person he knows best right now. You cannot give up on him."

"I'm not giving up on him," Clara shook her head with disbelief in her eyes.

"You are. Or you're unsure of whether or not you want to continue travelling with him just because it's not what you're use to seeing," Sherlock narrowed his eyes. "He's the same man. He shares the same memories, though just a tad jumbled now, but irrevocably all the same."

"His personality is different, it's like starting over," Clara tried to reason.

"You can't see him, can you? Not like this, and not now, anyway," Sherlock shook his head and looked at the TARDIS. "I can take care of him tonight, I don't expect he'll be ready to go for the morning. John can assist if anything medical related arises, though I'm not sure how much we know of Time Lord anatomy. If you don't feel quite safe in the TARDIS, there is a bedroom downstairs in 221c you may use."

Clara digested this information, not protesting a word he said, "thank you, Mr. Holmes."

"Sherlock, please. I have a feeling we may be more acquainted soon," Sherlock nodded. "Did you need any help retrieving some things in the TARDIS?"

"Yeah, perhaps. It might be safer having another person in there. You know the way through?" Clara stood up.

"I do."

Sherlock stood up and followed Clara, who cautiously creaked the door open. The smoke seemed to have dissipated for the most part and it almost looked like the TARDIS fixed itself.

"What happened exactly?" Sherlock neared the new console, his fingers brushing the smooth metal.

"He regenerated and we started crashing," Clara walked up the stairs to the new upper portion of the TARDIS. "I tried to pilot, but it was hard trying to concentrate."

"I can imagine," Sherlock muttered to himself, then turned around when he heard another pair of footsteps cautiously make their way inside the time machine. "John? What do you need?"

John was holding the pictures of Amy and Rory in his hands along with the box. He didn't say anything, but his face gave Sherlock all the unspoken things said.

"They've gone," Sherlock softly spoke.

"Yeah, I can see that," John half chuckled, looking at the box. "I'm not mad at her, Sherlock. I get why she didn't tell me. It's just that I wish that she did."

"Me too," Sherlock nodded.

"It's weird," John held up the photos. "I'm looking at her ghost. Her husband and her, they're gone and I couldn't even say goodbye."

John placed the photos inside the box and then placed it down on a chair. When he did so, he finally realized where he was, and had to take a step back to really look.

"I honestly can't believe this," John looked upwards. "How is this even possible?"

"Come on, let me show you something," Sherlock smiled, a curious expression growing on his face. "Clara?"

Clara was nowhere to be seen in the main space, so Sherlock shrugged and told John to follow him. Sherlock wanted to show John a few of the more interesting rooms housed in the TARDIS while Clara went to fetch her things, but it was the sound of the TARDIS in flight and the sudden jerking that alarmed the both of them.

"What's happening!?" John tried to balance himself as they jogged back to the main control room.

"I don't know! I think we're in flight!" Sherlock nearly crashed into Clara as they met in an intersecting hallway.

"What's going on?! Who's flying the TARDIS?!" Clara yelled as she tried to hold onto Sherlock for balance.

Sherlock, in the lead, managed to make it to the TARDIS controls first, only to see the newly regenerated Doctor pressing a series of random buttons and pulling every other lever.

"Doctor! Stop!" Sherlock called out.

For some reason, the Doctor listened to him and abruptly jumped away from the controls, but this did not help the wobbling time machine. Like a frightened cat or a scared child, the Doctor immediately raced outside and closed the door.

"Shouldn't we go after him?" John asked.

Clara went to the TV screen and turned it on, "oh, my god."

"What is it?" Sherlock asked as John neared the doors.

"We have to go, we have to go right now," Clara raced to the doors and burst through them.

From the glimpse that Sherlock got they were either far in the past or in the very distant future, and still among a lot of green foliage, but it was the TV screen that told him why they needed to leave immediately.

"John, brace yourself," Sherlock pressed a few buttons, and moved a few levers.

"Doctor!" Clara dragged the Doctor back in, who quickly took his spot by the TARDIS console, pushing Sherlock away and doing away with all the steps he took to fly back safely to London.

The Doctor sent the TARDIS in flight, albeit very bumpily, and Sherlock, Clara and John crashed into the railings hard, yet the Doctor still managed to stay glued to the controls. Somewhere over the course of the flight, something must have caught on fire or exploded as smoke was spewing out from the center controls. The TARDIS then stopped, but tilted heavily, its angle made it very hard to stand up straight, but it wasn't the Doctor's doing.

"What just happened?" John tried to steady himself. "Where are we?"

Sherlock coughed, "can we get out?"

"Shush!" the Doctor somehow managed to get into Sherlock's personal space and placed his hand over Sherlock's mouth. "Do you hear that?"

Sherlock shook his head as the Doctor kept his hand on Sherlock's face.

"She's choking."

"Who's choking?" John asked, frazzled.

"Big woman. BIG woman," the Doctor laughed.

Unexpectedly, the TARDIS jerked forward again and gravity seemed to have failed them for a moment, for all four of them were hovering high in the air for a few seconds before the TARDIS crash-landed into the sand. The crash accidentally knocked Sherlock out, while John managed to sustain only a few bruises. Clara managed to land upright, but still dishevelled, after grasping tightly to something.

"Sherlock? Can you hear me?" John tried to lightly shake Sherlock awake, but it was doing nothing.

"Where are we?" Clara coughed, adjusting her cardigan.

The Doctor didn't respond, instead, clicked and pushed more random buttons before a knock at the TARDIS doors interrupted.

"Hello? Exit the box, and surrender to the glory of the Sontaran empire!" a muffled voice was heard on the other side of the door, and the Doctor rushed to it, opening it and shushing whoever was there.

"Doctor?"

The Doctor opened the door again and addressed Strax, though neither Sherlock, John, or Clara could see him, " I was being chased by a giant dinosaur, but I think I managed to give it the slip."

"Dinosaur?" John mumbled, his attention turning towards the Doctor.

The Doctor exited the TARDIS, leaving John with Sherlock while Clara stood there confused and unsure of what to do, but she decided her next course of action was to step outside and see where they were.

"Is he okay?" Clara asked before walking towards the door.

"He must have hit his head, but he looks fine and anything that would break hasn't broken, so there's nothing I can do right now," John saw what she was doing and immediately went to her. "Where are you going?"

"Finding out where we are," Clara spoke without looking at him, instead opening the door to a dreary day in Victorian London.

Sherlock began to grumble as he started to regain consciousness and John turned his attention back to him, "don't get up too fast. You just hit your head."

"Where are …," Sherlock spoke dazedly.

"London," John twisted his head to look out the door. "Victorian London."

"Oh, that's good, Watson," Sherlock patted John's shoulder before collapsing into unconsciousness once again.

Not quite sure what to do John stepped out of the time machine and onto the gravel outside, but it was the commotion coming from the Doctor and a roaring dinosaur that distracted him from the unconscious Sherlock laying in the TARDIS. Suddenly, the Doctor's face was just inches away from him.

"Clara, tell Handles to turn down the frequency of the sonic lanterns," the Doctor spoke frantically.

"He's not Clara, I'm Clara," she tried to explain.

"Well, you're very similar heights. Maybe you should wear labels?" the Doctor looked back and forth between Clara and John. "Wait, why are you all doing that? You're all going dark and wobbly. Stop that."

The Doctor, swaying, closed his eyes and collapsed right into the sand. John instantly went to him to check and see if he was all right.

"What do we do?" John asked, now noticing the lizard woman and the potato-looking alien in a suit. "He keeps collapsing."

"I don't understand. Who is he? Where's the Doctor?" Jenny asked Clara.

"Right here. That's him. That's the Doctor," Clara clarified to confused looks.

Vastra sighed, shaking her head amusingly, "well then, here we go again. Strax, get the carriage. We are not carrying him back home."

"Them," John spoke suddenly.

"Sorry?" Vastra looked at John.

"My friend, he's unconscious in that box," John looked back at the TARDIS.

"Well then, we'll have to make do, won't we," Strax looked at Jenny, who nodded. "Clara, if you could help bring his friend out here as well, that would be more than helpful."

Clara rubbed her face with her hand and John could sense the frustration coming off of her, "sure. Fine. Just give me a moment."

"I'll just be in there," John gestured to the TARDIS, but the statement fell on deaf ears as Clara walked away from the Doctor and the others went a different direction.

John went back to the TARDIS, sensing that Clara needed some space. Smoke no longer arose from the center of the console, and John sighed with relief at that. He did not want to die from smoke inhalation in Victorian London. John looked back at the open doors and watched the commotion for a moment, listening to the sounds of an impossible time period that he never would have come upon.

"Definitely a bit different from my day," John shook his head and smiled.

John passed the box of items once belonging to Amy and Rory and smiled sadly. All of this – the time machine, travelling forwards and backwards in time – is what they had seen and lived, and though he was still disappointed he never got to hear it from Amy, he understood why she wanted to wait to tell him, he understood that she was never really normal. Coming upon Sherlock's body, he rolled his eyes and chuckled at all that Sherlock was missing.

"You better wake up soon, Holmes," John smiled as he looked down at Sherlock. "After all, this is the 19th century."

The Sherlock Complex will conclude with an Epilogue early January 2016, but till then, thanks for reading :)