Don't own Matrix.

This is the final chapter of Against Protocol. It's been fun, but it had to end eventually. Review please, since I can always go back and change stuff.

It ends with an idea for a sequel...tell me what you think about that specifically.

Thanks, enjoy.

“Systems normal,” Elise breathed her lungs full of air again, trying to calm her nerves as she watched the Nebechanezzer rise, living them to either certain death if Elise didn’t live up to Morpheus’s unfairly high expectations.

“All pads are go,” Browser, her new captain, flipped a switch above his head, and pulled a lever.

Elise felt the back of her neck go balmy, and butterflies in her stomach rise like a violent storm. Morpheus could have at least left them with Tank or Dozer. Elise found herself praying whatever the Oracle was, that she and Morpheus were right and they’d make it through this.

From the Nebechanezzer, Browser and Elise watched Morpheus and Dozer wave, Dozer mouthing the words “good luck”.

“We’re on our own now, huh?” Browser asked, as Elise grabbed the controls, bracing herself against her harness.

You don’t have anything to complain about, Morpheus brought the worst job on Browser. She glanced at him from the corner of her eye, the new captain of the follower. Browser’s tan face was stern and controlled, ready for this much more than she was.

“Yep.” Elise flared her nostrils, her blood pounding in her head.

Browser touched her arm, making her turn, surprised at the touch. “We’ll be fine. I promise.”

Elise nodded, looking back out the front window. She pushed a button, and the lever on her side, and the Follower began to rise from the ground.

“Here we go.” Flash spoke quietly behind them. She and Chip were waiting in silent support, Flash, strapped into the seat behind Browser, and Chip holding onto the handle connected to the ceiling.

As the ship rose, and Elise turned it towards the exit, she laughed with relief near hysteria at how simple it was…like driving a car.

After about twenty minutes, Morpheus called. Chip explained the scenario, and Morpheus told them, since the Nebechanezzer was faster, that they’d go on ahead to Zion since Elise and Browser were fine controlling the Follower. He said it would attract less attention from the Sentinels. “Don’t want to blow our EMPs in rage of each other.”

“This isn’t so bad.” Elise smiled, feeling the first sense of power since she’d left the Matrix. “Maybe the Oracle was—”

Then something happened that made Elise stop, and the smile fall from her face. The steering wheel turned, without her touching it, heading the opposite way, away from Zion.

Elise grasped the controls, trying to turn it back around, to no avail. “Browser.” She struggled against the machine.

Browser’s head turned, his face confused. “Why’re you turning us a—”

“Help!” Elise pleaded, unsure of what was happening.

Browser’s arms grabbed the control handles above where hers clutched it, and tried to tug it towards him.

“Stop the hover craft,” Elise ordered, her voice strained, without really caring she was giving an order to her superior.

“What?”

“Stop the ship!” she yelled.

Browser let go of the controls, and flicked a switch, pushed the lever, but none of the lights went out, and the ship kept moving right along. “Oh…no…” Browser’s eyes fell on the EMP…that had gone black. “Flash! Chip!” He unclasped himself, scrambling out of his seat, running down the hallway to find the others.

Elise closed her eyes, clutching the controls, willing herself to move them. The ship straightened itself out, facing the other way, and nothing she did could change that. Giving up, she unclasped herself, following Browser down the hallway.

“Everything’s been overridden!” Elise yelled furiously from the suspended grating hallway. Browser and Flash were trying to get the bottom door open without any success, and Chip was in front of the Matrix feed, typing like a mad man. Every one of the screens had gone black.

Elise jumped down half the stairs, pulling the manual override that was supposed to shut off all power, but though she got the lever down, the lights only flickered for a moment. Someone had broken the wires connecting it, and they’d done it in such a way you couldn’t tell it was broken unless you pulled it.

“Dozer was right!” she yelled angrily. “It’s a trap.” She kicked the wall angrily. The Oracle had been wrong. Morpheus had been wrong. Now all four of them were going to die, they were going to be picked from the metal belly of the Follower by the Sentinels.

“They’ll take us to Zero-One,” Flash snarled, pulling at her short hair.

“I can’t call Morpheus!” Chip called. “The whole Matrix signal, and the phones are dead.”

“Chip! The radio!” Host called.

Chip nodded, scrambling up to the cockpit, with Browser and Host two steps behind him. Chip pressed the button, his face close to the microphone, “Hello? Hello? Come in, Nebechanezzer! The ship’s malfunctioning!”

“Wait.” Browser’s big hands stopped Chip, listening to the feed from the radio. Browser’s mouth, closed to a tight line, twitched with fury. “It’s the engine room.” Browser was gone again, jogging down to the engine room, where Host stumbled to keep up with him. Browser slammed down on the button, his nostrils flared. “Hello? Hello? This is the Follower we are—”

“No good,” Chip replied from the other side. “I can’t switch channels. The radios been tampered with. We can only get each other.”

“I know!” Browser bellowed, his voice dark and strong and furious as a grizzly bear.

“The access codes!” Host called to him, from across the room, where she’d wandered to get away from his furiousness.

Browser pulled a folded piece of paper out from his shoe, looking at it with sudden sorrow.

“If they take us, they’ll be able to hack your mind, get the codes out.” Flash lifted her head, walking towards Browser.

“I haven’t even glanced at it,” Browser assured them, and he hadn’t. Elise’s eyes fell on the folded piece of paper with misery. “Don’t need this anymore.” He shrugged, tearing it to bits.

“That isn’t going to keep the codes safe from them when they get us.” Chip picked up the scraps, and, with grimace, dropped them in his mouth, and chewed the ancient paper. “Just don’t tell me where it’s been.” He chewed the paper, swallowing hard with displeasure.

“You’re sure you never looked at it?” Flash demanded, stepping towards Browser, Flash’s hand touched the handle of the only gun they had, her eyes full of suspicion.

“He wouldn’t lie to protect himself sacrificing the whole human race!” Elise snapped.

“We’re all dead anyway, what does it matter?” Flash barked.

“Ladies!” Browser yelled, his voice echoing off the walls. “All that matters now is Zion. Host, Flash is right, it would be best if you k—”

“Browser!” She glared, rage concealing the despair that was coming. “So you want us to just fry you alive?”

“Zion’s all that matters,” Browser lowered his hands.

“You said you never even looked at the codes,” Elise spat with venom. How could Browser be so…so…

Flash looked at their captain, who was staring intently at Elise. “That’s right. I didn’t.”

“Good. Now we need to find some way out of this,” Elise’s voice became authoritative.

“EMP. We get to the center of Zero-One, and blow it—” Chip’s voice was heroic, but Browser shook his head.

“It’s been entirely disabled. This whole ship has been reengineered to trap people. I doubt there’s even an EMP inside it,” Browser’s face was concentrated on being calm, but the fury in it was clear.

Elise kicked the wall again, pulling a pipe off the wall with an furious scream, feeling herself loose it. Falling on the ground she pulled at her hair. It had grown to mid-ear length. This was how it was going to end. If not by Agents, than by Sentinels. Elise didn’t bother asking which was worse. Either way she was dead.

I’m sorry Smith…I’m so sorry…

In the background, Browser gave another groan of struggle as he tried to open up the door, Flash went for a run around the ship, looking for an escape, and found none. Every possible way out of the ship, that normal ships all had, had been reengineered by the Machines to fail. Chip was trying to get the Matrix feed back online to send a distress signal to the Nebechanezzer, but nothing would turn the monitors back on.

Elise didn’t care if her “captain needed her” anymore. Captain of what? Of a ship designed to trap people and carry them to the heart of the Machine City to be slaughtered? Every emotion she’d kept inside her since she learned of the Matrix, every emotion that had been amplified since what had happened six days before poured out of her. The dam didn’t burst, she just opened the floodgates, letting herself cry, which she had not done since the night she’d met Morpheus.

Smith…James…Smith…Tina…Smith…Becky…Smith…Jessica…Smith…oh Smith…I’m going to die, Smith…I’m going to die…I’m going to die, Smith…and…I love you…I’m sorry…I’m sorry, Smith…

…………………………………

Two hours later

……………………………

“Doesn’t it just take your breath away?” Chip asked miserably, his beady eyes staring out the front window with a mixture of astonishment, wonder and horror.

“Not the term I would have used, but yeah.” Elise stood next to him with Flash and Browser, staring down at the fields of humans. Just as Morpheus described it.

In the distance, mountains, as bleak and barren as the rest of Earth, loomed ahead, behind which came the eerie glow only the Machines made. Zero-One.

As they neared the city, the sky filled with Sentinels, and Elise held her breath as they flew next to the ship, like an entourage.

The Follower, whose name meant something different entirely than what it did when it was built, lowered itself to the ground, in what would be the streets of Zero-One.

Instead of continuing in Zero-One, however, the Follower, and the Sentinels turned off, heading towards the edge of the Machine City.

“What do you think they’re going to do to us?” Chip asked. He was less than eighteen years old. He was still a kid.

“Plug us back in, take us to the Agent’s Headquarters and torture us until we’re dead,” Flash answered, her lips curling with disgust.

The Agent’s Headquarters…

Elise turned away from the dismal picture in front of her, wanting to have some small amount of peace in her last moments. What if they were taken to the Agents in the Matrix? And…if the crew found out about her and… She didn’t want the last memories of her to be distorted with hate, she didn’t want them to know that she was so close to treason.

Would Smith be there? No, because of you he’s probably been deleted. Which to the Machines would be just like killing him…

…………………………………

Half an hour later

……………………

The ship stopped, when the two great claws grabbed each side, exactly where the dents had been, lifting it to what looked like a dock, and the bottom creaked open.

Every sound, every noise, every pair of lungs and beating heart was amplified, breaking the deadly silence. The crew had taken refuge in the engine room, the most secure place they had.

The metal clopping of “feet” echoed like a warning through the metal belly of the Follower. The Machines were coming. They wouldn’t send the Sentinels, they’d send the smaller robots, the ones people had created centuries before to look like people. It was disgusting.

The metal door had been locked and bolted from the inside, and the crew was huddle in the corner. Flash held the gun they’d brought from the Nebechanezzer, which was the only gun on board the ship, even though all of them were required to have at least one, if not two.

Browser was in front of Chip and Host, and next to Flash, to protect them.

The thumping of the AI’s came closer…and closer…and closer…

Then a greater noise came, and a giant dent appeared in the door, making the crew flinch back…and another…and another…and another.

The door fell, and Flash fired the gun as the metallic bodies forced their way in. Browser’s arms wound tighter around her and Chip, as Browser tried to kick away at one that leapt at Flash.

Elise felt that cold, twisting stab of pain in her stomach that was severe fear. She squeezed her eyes closed, trying to wake up and realize everything, Morpheus, the Matrix, the Follower, Agent Smith, James, trying to make everything just a bad dream, trying to find home.

Flash shrieked as she was yanked away. Chip’s cry came next, and her side was cold where he had been. She felt something like ice on her ankle, tugging her, but Browser held on, kicking at something, but then something came after him, and his warm arms fell away. The thing like ice came back, but now all over her, and she was pulled out, pulled somewhere. She wouldn’t allow herself to open her eyes, praying it was a dream, a nightmare, the worst she’d ever had. But some nightmares you can’t wake up from…

“This is the human?” a digital voice asked, a digital voice that sounded far too human.

“This is she. The Architect wants this one alive. The Source ordered us to be careful with this one.”

……………………………………………

Machine City, the far end

……………………

The four of them were lined up on some metal platform. There forearms, and legs were being held by some metal claws, not allowing them to move. In front of them, was the Machine City, in all of its filthy glory.

“Which one of you is the captain of the ship the Follower?” a deep voice asked from somewhere.

The crew went silent.

Elise’s vision was blurred, her mind unfocused and she felt a grim need to vomit, but the others looked much worse. Flash’s legs were cut up and bleeding, Chip had been knocked unconscious when he hit his head against the metal wall, and Browser…Browser looked worse than death. Compared to the others, they had been very gentle with Elise.

But why would they want her?

“Which one of you is the captain of the ship the Follower?” the voice asked again from somewhere in the very blurry scene. Maybe it was shock causing Elise’s eyes to haze over like that.

A surge of pain came from the metal bonds that held them, probably electricity.

“Which one of you is the captain of the ship the Follower?”

Again there was silence.

The dark form from which the voice must have been coming from sent a swarm of something that looked like giant flies to Elise’s eyes, which swarmed around Chip, causing him to yelp in a guttural voice.

“Which one of you is the captain of the ship the Follower?”

The swarm spread out, coming over all of them, slicing at their flesh, as the surge came again.

Browser opened his mouth to say something, but Elise was faster. “I am!” she screamed, one of the giant flies cutting at the side of her head, millimeters from her temples. Her voice was much louder than she would have ever thought she could make it, especially under such pain.

“You’re lying, human,” the voice didn’t change at all. “Do you know the access code to the Zion mainframe,” the voice demanded, speaking to all of them now.

“No,” each one of them answered in their own time, with encouragement of the tiny robots that sliced at their flesh.

“You speak the truth,” the voice concluded.

Flash tried to speak, but some Machines, Elise couldn’t be sure what they looked like or where they came from, but they came and took the crew, dragging their limp bodies off the metal platform.

Elise couldn’t be sure exactly what happened after that, because everything went black, and the world faded into a gray mist, and all of the sounds disappeared into a steady beeping.

Beep…beep…beep…beep…beep.

…………………………

Two days later

………………

Beep…beep…beep…beep.A digital noise kept rythme, steady, and annoying as an alarm clock.

Elise’s eyes were heavy, and she wanted to sleep. Whatever this soft thing was, it was nice…and warm. There was a light on the other side of her eyelids, something bright, and warm. The sun?

Her body ached, and she slowly became aware of things stuck into her.

With a groan of pain she opened her eyes, blinking in the sunlight, pouring through the window.

Rubbing her eyes, she realized there were IV’s connected to her arms, and the beeping was a heart rate monitor. A hospital?

The walls of the room were pale blue, and what she lay in was a bed. Somehow her rags had disappeared and she was wearing a hospital gown instead.

The foggy feeling in her head must have been pain killers, but she was able to think clearly enough to know this wasn’t good. There was nothing like this in the real world, and the sun was outside.

Oh no… Elise’s heart started off sprinting as she became aware of what had happened. Desperately, she tried to pull the IV’s out, trying to get out of this hospital bed, when someone stopped her. Two arms, one on either side, belonging to two different people, pulled her back down against the bed.

“Stay still, Miss Roberts,” one of the men ordered.

Elise’s head rose to see Jones, his face expressionless, standing over her. The other “man” was Brown, and both had their guns.

Elise’s mind raced with every curse word she knew repeated over and over on top of each other set to music and screamed out internally.

“You aren’t well,” Brown added.

Elise suddenly felt very sick and very speechless. If she was here, where were the others?

“The others have been reinserted as cripples.” Jones read her mind.

“They remember nothing,” Brown said over the end of Jones’s words.

“They can hardly speak,” Jones turned his head slightly to the side, intimidating Elise, and making her pull the thin hospital blankets up higher despite herself.

“As you will he finishes his questions,” Brown assured her.

“He wants you to be healthy by then, so it would be in your best interest if you did not attempt to run, as we would have to take certain measures into hand,” Jones threatened.

“Run?” a dry chuckle sounded from somewhere behind Jones…a dry chuckle that made her heart stop and nearly pound out of her chest. “There is no way out of this building until the Architect says you can go, and he will say you can go when you give him what he wants.”

“Smith?” Elise knew that was impossible…but she’d know that voice anywhere. Maybe it was the painkillers, affecting her process.

“Yes,” a different voice answered, seemingly amused. A man, with a white beard, a white suit, white shoes and a very pale face stepped through the door. “But don’t waste your time, Miss Roberts. The virus has been eliminated.”

“…What?”

“His memory’s been wiped clean, but that’s a different matter.” The man took a seat in the chair by the hospital bed, a plain white leather arm chair, and picked up a small clipboard. “Leave us,” he ordered, his eyes focused on the clipboard. The Agents she could see, Jones and Brown nodded, seeming to drift to the door, instead of walking. They were followed by another, who had to be Smith, but Elise couldn’t see his face, and he didn’t turn to look back. Why wouldn’t he just look at her?!

“Smith!” she yelled, but none of the figures even hesitated as they left the room. “Damn it, Smith! Smith!” Elise screamed as the door closed behind the Agents.

“He doesn’t remember, I told you.” The man was still examining his clipboard, testing out the ink of a pen on the paper, his voice monotone, but mocking.

“What?!” Elise snapped.

“I told you, Miss Roberts, Agent Smith doesn’t remember a thing about you.” The Architect smiled a smug smirking smile that made Elise want to rip his throat out. It was such a nice thought, she tried it, lunging forward, but found she was attached the hospital bed by some belt around her waste.

The Architect raised an eyebrow at her, and pressed a small button on the side of her bed, sending some silver liquid through the IV’s into her blood, giving her a sudden blurry feeling, making her whole body go numb.

“Now, let’s get down to business, shall we?”

……………………………

The next day

…………………

The Architect stood before a white board, watching the inward workings of his mind play out on it. The equation didn’t make sense, it just didn’t add up. There was a missing factor in it, but no matter how many times he questioned the human, he couldn’t find a plausible answer. It didn’t make any sense!

For a program to behave in such a human matter was unheard of! It didn’t make sense.

The Architect became very frustrated, infuriated by the idea of his grand master piece being defeated by a simple human woman! It was impossible!

When he’d finished his questions with her, coming up with nothing, he had done to her what he’d done to the other three in the ship they’d captured. He’d reinserted her into the Matrix without any memory of what had happened. She’d stumbled back into her life, the way it’d been before she’d heard of the Matrix, everyone believing she’d just had an incredibly powerful case of amnesia.

At least it had all come right. Smith was back to normal, and the human’s knowledge of the Matrix had been sucked away, deleted from her mind as easily as if she were a program herself.

But it didn’t add up! He couldn’t leave the problem unfinished! It was impossible to leave it undone like this!

The Architect went over the equation again and again and again and came up with “x = ?” every single time. He couldn’t find the missing equation. It was hopeless.

At least the human will never again pose a threat to the Matrix. Even her insolent “friends” have no memory of Smith…but how…? How is it possible?

………………………………………………

Somewhere in the city

…………………………………

“Amnesia?!” Mr. Dutton barked, his voice as angry as ever.

Elise nodded, handing him the notice from the doctor. One day she’d fallen asleep, the next thing she knew, she was in a Kaiser Hospital, with nurses and doctors buzzing around her, talking about massive brain injuries that had caused her to fall into a coma for almost three months.

It didn’t make sense…she remembered everything perfectly before her accident (falling from an open window), but afterwards…it was a blank. No, not entirely perfect, there was a giant part missing…something to do with her deceased husband was gone…all the details of his death were foggy in her mind, but Tina assured her that they’d caught the killer, a man named Ralph, who denied ever even knowing James.

“I’m sorry sir, I—” Elise tried to speak to her boss.

“Get back to work, Roberts!” he bellowed.

…………………………

Across the city

……………

Humans.

How he hated them.

Their stench seemed to stick to everything.

That odor. That horrible smell he couldn’t free himself from.

Even here, surrounded by other Agents, the smell lingered. Like germs. Mimicking the parasites they came from.

Humans.

Agent Smith hated them. Every one of them was disgusting and worthless.

………………………………

The next day

…………………

Agent Smith didn’t like the way the others were acting around him. It was unnatural. They acted as if he were diseased, avoiding him as often as he could.

He preferred to be alone. He was faster alone. He was much more efficient that way.

It was a day in early spring. The Resistance were being quiet again, which annoyed him thoroughly, so he went out to find something to do, whether it was against protocol or not.

Instead of taking the Audi, which he knew, for some reason, was bugged, though he couldn’t imagine why they’d bug his car, as if he ever did anything wrong, he decided to walk among the filthy parasites instead.

It was still chilly in the Matrix, so there were less of them around.

He came to a park, his eyes scanning the place for possible criminals to destroy, but found nothing.

The park was what separated the human city’s “rich” side from the “poor” side, and so there was always a good chance of muggers to kill, so he walked along the path, his eyes darting around the empty place with a hunger.

As he came around a corner, out of a grove of trees, his eyes found a figure on a bench, a woman, watching the bird programs.

…That was strange…there was something about the woman…he didn’t know what it was, but something about her reddish brown hair made him slow his pace.

The woman raised her head as he passed, eyeing her, but when he saw her look back at him, he stopped entirely, furrowing his brow at the look.

The woman looked almost lost when she looked at him, with an almost childlike wonder. “Excuse me, sir,” the woman rose from her seat, “but, don’t I know you?”

Agent Smith didn’t know what told him to, but slowly, as the woman took a step towards him, he removed his sunglasses with his usual inhuman grace.

Green eyes looked into blue eyes, and they knew the other remembered everything. A thousand thoughts went through both minds, with enough force to knock most people off their feet. Like watching their lives flash before their eyes, they remembered.

“No. No you don't, Elise Roberts.”

THE END

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