Sylar wasn't scared. He wasn't. He couldn't be. He could heal himself, he could shoot lightning from his fingertips, he could fly. What could this 'Doctor' do? Nothing! He had two hearts. He had a TARDIS. That was all. He was completely reliant on this blue box of his. He did not have the power that Sylar did.

But that did not stop Sylar from pacing nervously, going in never-ending circles as he went. His thoughts were racing. Would the Doctor leave him alone? No, the Time Lord knew that Sylar was a threat. He would find him, chase him down.

So what should he do? Should he run? Should he try to hide from him? A man who was powerless, defenseless, a man who couldn't stop him from ripping open his head and searching the depths inside? Should he just run, get as far away from this man who could do nothing to him?

But no matter how hard Sylar tried to convince himself that the Doctor was weak, it could not be done. A fear that he'd never known had gripped his heart. A strange, unnatural chill was slowly spreading through his body. His legs felt weak and strange, as though they would not obey his commands when he needed them most. His arms were tingling as the nerves were stretched to their limit.

He stopped. So would he do it? Would he run?

And give the Doctor the satisfaction of scaring him off?

"Never!" Sylar was unaware that he had spoken the word out loud until it reached his ears. He jumped; further proof that he was more on edge than he had ever been.

So what could he do? Stay and fight? It seemed the only other way, the only other option.

And yet, Sylar knew he would not win. He knew that it would be impossible for him to destroy The Doctor. For all of his abilities, for all of his powers, for all his strength, and for all of the Doctor's weaknesses, Sylar would lose.

Sylar's mind kept spinning as he began to pace once more. How many others had fallen into the same trap as he had? How many others, on how many different worlds and in how many different times, how many? How many of them had believed that they could destroy the Time Lord, only to end up here? Deciding whether to run and hide or stay and fight, when they knew that either choice would be their end? How many of them had chosen to run, and how many chose to fight?

Sylar wasn't sure what would happen to him if and when the Doctor won. Would he be killed? It wasn't really possible. The Doctor knew that.

Though there was one spot, on the back of his head. Sylar gently placed his hand on it, as though that could protect it.

Would he be condemned to live the rest of his existence in a cage, a prison that he could not escape? He had spent some time imprisoned by the Company, and had no real inclination to be in that situation again.

Death or imprisonment? Sylar knew that he could not be in a cage unless his abilities were rendered useless. Or the cage was strong enough to hold him. Either way, his abilities would mean nothing to him. He would be… Powerless.

Sylar cringed at the very thought. He'd rather die.

And there it was. The decision. As quickly as the thoughts had come, they were resolved. He would stay and fight. And if he lost, he'd die. Or hope to die, rather than be forced into a cage.

His thoughts, his questions, no longer tortured him. He sat down, perfectly calm. Now that the decision was made, there was nothing else for him to do.

He relaxed, waiting for the Time Lord to come.

The Doctor, like always, was thinking.

He paced the room, six pairs of eyes watching him as he did so.

"So…" Peter spoke at last. "What are we going to do about Sylar?"

The Doctor's eyes flickered over to him. Peter looked down, uncomfortable under his intense gaze.

"Sylar?" The Doctor asked. He looked genuinely puzzled for a moment, then seemed to remember suddenly. "Oh! Right! Him!" He waved an airy hand. "We can deal with him later. What I'm really concerned about is this."

The Doctor pulled the knife out of his bigger-on-the-inside pocket.

"A knife?" Matt asked.

"Not just any knife, my dear telepath. The knife that stabbed me. The knife that is absolutely covered in DNA and fingerprints."

"Yeah." Peter rolled his eyes. "Sylar's. Obviously. So why are we still here?"

The Doctor shook his head. "No, no, no, you're missing the point. Think! Sylar used his regenerating blood to fix up the knife wound, remember?"

"I'm supposed to know this how, exactly?" Peter demanded, irritated. "You haven't really told us anything. You just pop by in that box and expect us to believe that you're an alien. Granted, circumstances are strange, but I've seen far stranger."

The Doctor blew him off again. "Yes, yes, all right. The important thing is that he did fix the wound, and he pulled out the knife. That would explain why his DNA is on the handle. But, here's the question: Why would he stab me, only to fix everything again?"

"Unless he didn't." Donna completed for him.

"Exactly!" The Doctor smiled, though Donna noticed he didn't look directly at her. "Sylar didn't stab me. Someone else did."

"Who?" Ando asked.

"Well, that's why we're here, isn't it? I ran a little DNA scan and found something very… interesting." His eyes drifted to Donna. All other eyes slowly followed.

Donna raised her eyebrows. "Me? Doctor, you know I would never…"

"Sylar's a shape-shifter." Peter jumped to her defense, unsure of why he was doing so. "He could have taken her form, made it so that you trusted him…"

"I thought of that. Some sort of shape-shifter, or imposter…" He shook his head. "But I'm afraid not. The DNA is infused with background radiation; only a time traveler could have done it. And I mean a proper time traveler, not this 'travel-without-a-capsule' nonsense." He gestured to Hiro as he spoke, then looked back at Donna. "It is definitely Donna's DNA."

They sat there uncomfortably for a very long time. Donna swallowed.

"Doctor, you know I wouldn't…"

"I know."

"Then what…?"

"I don't know. Something happened. Something important, something that I've missed…" He pinched the bridge of his nose.

"Doctor, why would I do that?"

"I said I believed you, Donna. I know you didn't…"

"Shut up and let me speak. If I did do it –which I'm not saying I did- I would have had a reason. I mean, you irritate me, and I might slap you from time to time, but I'd never stab you. You're my ride home!"

The Doctor smiled, though a few of the heroes were shooting worried glances in her direction. "Yes, that I am." The Doctor started pacing frantically. "I wonder, though, if I'm doing the right thing, staying here, trying to work this out…" He trailed off, lost in thought.

Silence filled the air for a minute, then the Doctor suddenly shouted, "GOT IT!" And ran for the TARDIS.

Donna leapt to her feet and ran after him, but the doors shut in her face.

"Oi! Let me in, Space Man!"

"Nu-uh. You're staying out there. Where it's safe." The Doctor's voice came from inside the box.

"I am not! Let me in, you great piece of space junk!" She yanked on the door handle, but the TARDIS refused to let her inside.

"Donna, this is probably one of the most dangerous things I have ever done. And I'm doing it just to find one stupid little answer to one stupid little question." Donna could almost imagine his grin. "Isn't that brilliant?"

"NO! It is not 'brilliant'!" Donna pounded her fists on the door. "Doctor, where are you going?"

"Think about it, Donna! Just think! I'm no teleporter, so how did I follow Hiro after I was stabbed?"

"How would I know? And you're changing the subject!"

"Well, that's what I've got to find out, isn't it? Now, you stay there. And if any of you let her get hurt…" The Doctor's tone darkened as he addressed the heroes. "I will hold each and every one of you accountable. Well, then. BYE!"

Donna stepped back as a deep, groaning noise, like the harsh breath of a giant, sounded from deep within the TARDIS's engines. The light on top of the box flashed, and the box dematerialized in front of her.

"I'm going to kill him." Donna hissed through clenched teeth. She sighed and stumbled back onto the couch.

For a moment, no one said anything. Many of them were shooting nervous glances at Donna, as though unsure if she would become homicidal at any second. Others were working hard to avoid her gaze. Hiro was staring at the spot where the TARDIS had vanished, a child-like wonder in his eyes.

No one was looking at Molly. No one saw her intense gaze, locked on Donna Noble. No one really even remembered that she was there until she spoke.

"You aren't here." She said. Her voice was very quiet, but it made everyone jump nonetheless.

Donna raised an eyebrow. "I'm sorry?"

Molly looked at her. "You're no where. I can't find you."

Matt raised an eyebrow. "Why would you need to? You can see her…"

"But I can't find her." Molly insisted. "She's not here. She's no where."

Donna looked at her. "I'm standing right in front of you!"

"NO!" Molly was on her feet suddenly, glaring at Donna. "You're not here, don't you get it? You're NO WHERE!"

Sylar was waiting for the noise. The one that would signal his failure, his defeat. The strange sound that sent chills down his spine as the fabric of space and time was torn apart long enough to release a little blue box.

It did not startle or scare him. He didn't even care about it. It was an oddity, a simple little thing that announced the arrival of something much larger.

"I'm in here, Doctor." Sylar called.

The Doctor stared at the scanner, watching as the patterns shifted and changed. He stuck his index finger in his mouth, waiting for the bleeding to stop.

"Well, vaff's owff." The Doctor said around his finger. He took it out and corrected himself. "That's odd."

He looked at his finger, his eyes widening as he saw the crimson seeping out of the small pinprick he'd used to take a blood sample. He hurriedly stuffed his finger back in his mouth.

He stayed like that for a moment as the scanner blinked and beeped. Finally, he removed his finger, no longer in danger of it bleeding. "Now, that's odd. That's very, very odd. That's so odd, it's not odd. Except it is odd."

He shook his head, having thoroughly confused himself. "That's strange." He said instead. "Very strange. So strange…"

He trailed off, not wanting to go down that route again. Instead, he studied the scanner. "Now, why would my DNA be in flux like that?" He straightened, then tried the word out a few times. "Flux. Fl-u-ux. Flu-U-U-u-ux. Fluxuation!" He cried it out almost triumphantly.

He looked around, waiting for Donna to slap him out of it, then remembered that he'd left her behind. How could he have forgotten? She'd put up such a fight it wasn't even funny. He winced; he was going to pay very dearly for that little stunt, of that he was certain.

He hurriedly turned back to the scanner, trying to focus on one problem at a time.

"So, my DNA is going absolutely wacko." The Doctor thought out loud. "Question is, why? Why is it doing it? Why now? What's the reason?" He perked up. "Reason. Re-e-eas-s-s-son. REEEAAASSONN!"

He looked around, shrugged, then pressed a button.

"No use just wondering!" He said, energetically spinning a little dial, then twisting a handle. "Time to go and actually find out."

The TARDIS lurched into life, throwing him off his feet.

As the TARDIS landed, the Doctor stood up again, jumping up as quickly as he could. He took a look at the world outside; not much had changed. The room was full of carnage, ash, dust, and black burn marks.

He walked to the doors and opened them. They creaked slightly, but it was drowned out by another noise.

"I'm in here, Doctor."

The Doctor tried to find the menace behind the words, the hidden hatred in the killer's tone. But there was none. There was no challenge; the words were simply a statement of fact.

He walked to the other room, glass crunching beneath his feet as he did so. He slowly opened the door.

Sylar was sitting down, perfectly relaxed as he looked at the Doctor.

The killer smiled. "You're late."

The Doctor raised an eyebrow. "I am?"

Sylar gestured to a painting next to him. "Yes, yes you are. You were supposed to be here exactly three minutes ago." One of his eyebrows shot up as well. "Which is surprising. This ability is rarely wrong, and when it is, it's because the future has changed."

The Doctor smiled as he remembered; one of Sylar's abilities was painting the future. "Strange."

"Very." Sylar replied. His eyes observed everything, as though he was preparing himself to use anything and everything he could to defend himself. Though you wouldn't have known it by his stance; he was still sitting, still perfectly relaxed.

The Doctor looked at him for a long time. "You know why I'm here." It wasn't a question.

"Yes."

"You know that this can't happen any more."

"Of course."

"And you know that this has to end. Here and now. The killing, the murder, the senseless deaths… It has to stop."

"I understand." Sylar said the words nonchalantly. "However, you and I both know that it would be impossible for it to end that simply."

"Perhaps not, Sylar. I'm giving you a chance. Just stop. Stop killing, stop stealing these abilities. Is that so much to ask?"

Sylar's eyes narrowed. "Don't give me a second chance, Doctor. You and I both know how that would end."

The Doctor looked at him sadly. "I'm afraid I do."

There was silence for a minute.

"You know how things work." The Doctor said at last. "And that's part of why I'm here."

Sylar raised an eyebrow. "Oh?"

The Doctor's eyes locked on Sylar's. "Yes. I need to know… How I work."

Sylar looked at him, interest sparkling in his eyes. "All right, Time Lord. You've gotten me curious. What, exactly, are you saying?"

The Doctor looked at him. "Something changed. Something has been done that needs to be undone. And I need to find out what it is."

"And why are you telling me this?"

"Because you know what's changed. You know, or you will know." The Doctor closed his eyes, as though the words were causing him physical pain.

"I need you to look at the heart of the TARDIS."

A/N: Sorry about how short the chapter is; I had to end it here. The next one should be longer.