A/N: thanks for the review, Lordheaven :)

Trinity burst through the rear door of the warehouse with a loud bang. Morpheus followed close behind her as he called Link for a new exit point. The Doctor came a few steps after. His need to turn and look when the interior brick wall exploded revealing an Agent Smith in the dust cloud cost him a couple precious seconds.

Four sleek motorcycles waited for them in the alley. Trinity shed her vinyl overcoat, tossing tossed it to the ground as she mounted a motorcycle and motioned for the Doctor to ride with her. "Hope you like motorcycles," she said and fired up the bike's engine. The Doctor hopped on the bike behind her and wrapped his arms around her waist. "Sure!" he grinned, "I have a scooter." Trinity just shook her head with a sigh then asked Morpheus, sitting on his own motorcycle beside her, for the location of the exit point.

"Fifth and Seneca," Morpheus answered.

"That's far," she said with concern and pursed her lips.

"Well, what are we sitting around here for?" the Doctor said with the excitement of boy on a carnival ride, "Allons-y!"

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The motorcycles roared as they sped down of the alley. Behind them, Agent Smith blew the door of the warehouse off its hinges sending it slamming into the building across the way. He stepped into the alley in time to see his quarry disappear around the corner onto the street. Before he could take a step, Neo slammed into him at full speed that sent him crashing helplessly through the building.

Without wasting any time, Neo launched himself into the sky and flew after the motorcycles.

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As Morpheus, Trinity and the Doctor sped down the street weaving around cars and completely ignoring traffic signals, the Time Lord was having a blast. The wide grin on his face hadn't faltered, though he did wish he had his glasses to help keep the wind out his eyes. To his surprise, his dark framed glasses suddenly appeared on his face. He thought about this and deduced that since he was now aware of the Matrix and himself, he could control it like Neo could.

As a test, he envisioned himself on the motorcycle with his tan overcoat flowing behind him like a cape. He looked down and sure enough, he was now wearing the coat. With an ecstatic laugh, he shouted, "Brilliant!" Trinity, who was focused intently on driving the motorcycle, called out to him over her shoulder. "I'll show you later," he beamed.

Behind the motorcyclists there was a cringe worthy crunch that drew the Doctor's attention. He looked behind and watched a crumpled car fly at an impossible speed toward them. It was going to hit them, he judged from its trajectory. He swallowed, unsure what to do, when the car suddenly stopped in mid-air. An airborne Neo swung it around and slammed it into a pursuing Agent Smith, knocking the virus into the pavement. A dozen more Smiths jumped into a pile on top of Neo dragging him down to the ground.

Trinity yelped and swerved the bike hard. The Doctor whipped his head around in time to see an Agent Smith standing in front of them. Trinity tried to earn some distance from the agent, but it wasn't enough. Agent Smith managed to grab the Doctor by his collar and yank him off the bike. To the Doctor, he felt like he hit a brick wall and even felt his body suspended in mid-air a long moment before getting slammed hard into the pavement.

The Time Lord lay on his back in a small crater, pinned to the ground under the incredible strength of Agent Smith's hand wrapped his neck. "We meet again, Mr. Smith," the agent growled with a dark smile and slowly lifted the Doctor up to his feet. The virus flattened his free hand and pulled it back.

"Sorry," the Doctor smiled tauntingly, "No Smith here, just the Doctor." He thought about how this person was not a person, but a computer program, and that his sonic screwdriver could scramble that program. The agent paused long enough for the Doctor to feel the sonic appear in his hand and activate it.

Agent Smith's face contorted in pain, and he howled in fury. He released the Doctor and doubled over as his code scattered back into the Matrix. The poor woman standing in Agent Smith's place closed her eyes and collapsed to the ground. The Doctor lunged forward and caught her in his arms. Gently, he lowered the woman to the ground and checked her vitals. He knew she was dead before doing that, but he held out hope that what Morpheus said about the take over wasn't true.

He frowned with sadness as he looked at the dead woman's face. "I'm sorry," he whispered. A motorcycle roared up beside him, and he looked up to see Trinity. "Are you alright?" she asked. He nodded and looked toward Neo with a clenched jaw. The One stood in the middle of dozens of Agent Smiths, punching, kicking, and killing them like they were meaningless playthings. The Doctor felt his rage well up inside him at the thought that each of those agents is an innocent human being.

Of course, he knew Neo knew this, but to Neo and his allies, this was war and these people were unfortunate causalities of that war. However, it wasn't Neo's fault. He and the others were driven to this in a desperate attempt to stay alive, to survive. And it was all because of some alien that was only interested in harvesting energy for itself. He climbed back onto the motorcycle with Trinity. "Let's get to that exit point," he said.

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A few minutes later, they arrived at the exit point, a simple public phone booth on a not so busy side street in downtown. Neo was able to clear the path of Agent Smith's and the virus eventually ceased his attacks. Trinity parked the motorcycle, and the Doctor climbed off the bike. His spiky hair stood on end and he looked liked he'd just had the best experience of his life. "I'd say let's do that again," he grinned, then turned serious, "but there's lives at stake."

Morpheus dismounted his bike and stood in front of the Doctor. "You weren't wearing the coat when we left the warehouse," Morpheus asked in a tone of cool observation.

"Yes, well," he put a hand on the back of his head and raised his eyebrows, "it seems I can make things appear when I need them."

"That could prove very useful," said Morpheus.

"It is rather brilliant, isn't it?" grinned the Doctor, "but I'll be much more useful in the real word."

"What did you do that agent?" Trinity asked as she slid off the bike.

"I thought of him as what he really is, computer code," the Time Lord answered casually, "my sonic screwdriver can scramble code and when it materialized in my hand, I used it. So, where's the exit?"

Morpheus motioned to the phone booth. The Time Lord couldn't contain his amusement. "Noooo, really? Oh, that's lovely," he laughed as he walked up to the phone booth. "I just can't seem to get away from phone boxes. And this one's even blue! How does it work?"

"For us," Morpheus indicated himself and Trinity, "it's a simple phone call, but you must swallow the red pill."

The Doctor dug into his pocket and held up the red pill to the sonic. "What does it do?" he asked looking at the pill with curiosity when the sonic didn't tell him anything.

"It's a script that disconnects you from the Matrix," Morpheus explained, "You will awaken in the power plant, and you will be flushed, but the script embeds a signal in your implants that we can trace."

The Doctor nodded slowly as he processed the information and mentally examined possibilities. "Implants," he smiled brightly with realization. "Of course!" he exclaimed snapping his fingers, "That's why my integration into the Matrix failed. I never really had a chance to think about it until now, but ooohh what a mistake the Source has made with me!"

"What do you mean?" asked Trinity.

"Being the Time Lord that I am," he held up a pointing finger, "my body just can't do with implants and is really good at rejecting the lot of em. I imagine the machines have been rather busy keeping them in place. That would explain the dreams I had of being in that pod…I was really waking up! Tell me you can take the implants out?'

"When we have you on board our ship," Morpheus said with reassurance, "we'll be able to remove all of them except the one in your head."

"You have to remove that one too," said the Doctor in all seriousness.

"We can't," Trinity said, "but Neo is coming and we have to go."

The Doctor grabbed Trinity by the shoulders and looked her in eye, "Listen to me, Trinity. You must remove all the implants, or I will be stuck in a healing coma until you do." He paused and held his hard gaze until she nodded.

He let her shoulders go and took a step back just as Neo landed a few feet away. He quickly strode over to the trio and said, "I've cleared the area, but it won't stay safe for long." He looked at the Doctor, "You must swallow the red pill now. I will stay here until everyone is out."

With a deep breath, the Time Lord looked at the red pill in his hand. He hated taking pills, but at least this one wasn't a real one. He looked between Neo, Trinity and Morpheus, "I'll probably be in that coma when you find me, and it may even look like I'm dead, but take out all the implants and I'll be fine. Try not to let me lose too much blood. I'm the only Time Lord left so you won't be able to ask for a transfusion."

The three nodded and Neo rested his hand on the Doctor's shoulder. "Don't worry, Doctor," he said, "we'll take care of you."

With a deep breath, the Time Lord lifted the pill to his mouth and paused. "I almost forgot," he raised an eyebrow and reiterated his words with his hand, "do not, under any circumstances, give me any pain killers, especially of all things aspirin. It'll be the death of me. Got it?"

"Completely," Neo said evenly and Trinity nodded.

"Alight," he said. He dreaded taking the pill, but he knew he had too. With a shrug of his shoulder, he popped the red pill in his mouth and looked at Neo with a cheeky smile. "Allons-y," he said casually with a hint of excitement and swallowed.

Next chapter, back to the real world!