Ghost in the Machine

Preview: Despite Neo’s considerable powers within the Matrix, he and his new found family group are no more than human in the real world, which is where the latest battles with the machines are being fought.

Rated G

Disclaimer: The Matrix, all characters and images therein, as well as story elements put forth in the movie are the property
of Warner Brothers and Village Roadshow Pictures. Several characters appearing in this story are my own creation. Any similarity with anyone living or dead is purely coincidental.

Authors notes: This story takes place approximately six months after the end of the movie. Again, my thanks go out to my fabulous Beta reader, Janet Spruill White. She’s continuously working to improve and fine tune my stories and deserves a great deal of credit for the work she’s put into it. Please feel free to drop her a line, at this address: size1 width100 noshade>

Ghost in the Machine

Trinity pushed forward, elbowing people aside, to get a better view of the monitor screens before her. The entire Nebuchadnezzar crew had gathered to see what the outcome would be of this last daring (some said insane) plan of Neo’s. If it didn’t work, they would have toiled and lost two members dear to them for nothing, but if it did…

A hand came down on her shoulder and she turned to see that Neo stood beside her, having noted her last minute entrance and made his way through the gathered crowd. “I thought you wouldn’t show,” he said.

“Yeah, well I’m still against this – don’t doubt that. I think that we’re putting our necks on the block.”

“It’ll work,” he replied, turning to look at the screen before him. “And if not, we simply destroy him.”

She looked at him, certain that it was not so simple as that.

He came back to himself to discover that he stood in a vast, empty plane. There were no walls, no ceiling, and actually, no floor.

In a way, it was strangely fitting, as he was not a he. He was not a man nor even a human being. Still, he found his current situation most curious – distressing even. His earphone was gone and so were his glasses. The voices of his fellow agents were gone, as well as the direction of the master programs.

The last thing he remembered was his subway fight with Anderson. He had been following him out of the subterranean complex – and then, suddenly, he was here.

Was he dead?

Did an artificially created intelligence have hope of an afterlife? Surely not! The master program had never been one for the theological and although he himself had occasionally pondered the question during his never-ending bondage within the system, he had come to the conclusion that the answer was no. There was no evidence – no proof of any sort that the intellect continued on after death, electronic or biological.

There was a noise behind him and he turned to find a large man in a leather duster standing there. Tall and dark in contrast to his surroundings, he was a presence which could not be ignored.

“Morpheus,” he said flatly.

“Agent Smith,” the cyberwizard responded. “You are, no doubt, wondering where you are.”

“Indeed.” He walked slowly around Morpheus, sized him up and came to a disturbing conclusion. “Am I a prisoner?”

“Yes. But we prefer to call you our guest.”


“We’ll come back to that in a moment.” Morpheus walked slowly towards him, stopping only two feet away so that he could, in turn, size him up. “It’s amazing, really,” he said. “You seem so human, right down to the wrinkles which appear around your mouth, not to mention the narrowing of your eyes when you’re annoyed – as you are right now. You don’t like being compared to a human – being reminded of how much like us you’ve grown to be.”

Smith found himself gritting his teeth. “Get to the point,” he ground out.

The cyberwizard tilted his head curiously and made a small noise. Then he straightened and moved away a few paces. “The point is that you were destroyed within the Matrix by Neo over six months ago,” he announced as he began pacing slowly around him, a maneuver Smith was well acquainted with – one designed to intimidate one’s prisoner. “We’ve managed to discover a previously ‘saved’ copy of ‘you’ in one of the remote locations of the system.”

Suddenly Morpheus moved closer and leaned forward so that his face was very close to the Agent’s own, but did not directly face him. It was turned away so that he was looking off into the infinite distance of the white cyberspace. The maneuver both startled and confused him. If he were human, he would say it made him… nervous.

“There was no way to access the files remotely, not even with Neo’s abilities,” Morpheus whispered. “It seems that for some reason we could not at first fathom, all lines in and out of this particular location had been intentionally disabled by our enemies sometime after your destruction. Still, the facility was under tight security, as are virtually all the Matrix subunits. We lost two good people breaking in so that we might obtain you.” Morpheus smiled sourly and looked directly at him. “Do you wish to guess why that facility was sealed, Agent Smith?”

“I do not make guesses,” he replied defensively. “That is a human trait. Besides, I have no knowledge of this facility you speak of.”

The dark man nodded and appeared disappointed. “Just as well, I suppose, as I seriously doubt that you could possibly correctly ascertain the reason.”

Suddenly two wing back chairs appeared along with an old television set. Morpheus gestured to one as he sat in the other.

Deciding to humor him, Smith sat as well.

Picking up a remote, the rebel leader pointed it at the set. “This is what we found,” he whispered.

Instantly, a picture sprang to life upon the screen. There, lying upon a flat, hard table, was a man. He was naked, bright, lights around him providing him with a comfortably warm envelope of air. His eyes were hidden by dark goggles and his hair, though long, could not disguise the fact that its scalp line was receding. He had no shunts or implants of any type attached to his body.

There was something wrong with the picture, though. The man…

Smith felt himself rising to his feet as he realized who he was looking at.

Trinity watched the monitor with amazement as the agent stood, his arched brows becoming even more prominent and giving him an expression of deep shock. Perhaps Morpheus and Neo were right about him – perhaps he had grown more like them than unlike…

“That is not me,” the agent responded, as his face again assumed its usual bland expression. When he spoke again, his voice was once more flat and even. “Your little ploy will not work. I am not human – I never was. I am an artificial intelligence which lives exclusively within the confines of the Matrix, or in this case, one of your computer systems.” He turned towards Morpheus. “I am, however, most curious as to what you are attempting to do here.”

Their leader also affected a bland expression. “No one is attempting to trick you, Smith. The fact of the matter is that your side is losing the war within the Matrix. Every day more and more humans awaken – more resistance cells spring up. The Agents are literally becoming overwhelmed and thanks to Neo, they are destroyed virtually as quickly as they are created. The machines know that they are losing control over their batteries and have now taken greater steps at attempting to eliminate us from the real world. Given that everything they’ve set against us so far is vulnerable to our EMP’s, what do you suppose the next step in this war is?”

Smith sank back into the chair. “No. They wouldn’t. It goes against everything…”

Morpheus interrupted him. “How deliciously ironic it is to see that the same mechanical masters which insist we are past our time in the evolutionary scale, indirectly turn around and admit that the human form is still the most complex and amazing of biological machines. Oh yes, Smith, this body is meant for you. We can only guess that your masters combed through their human stock until they found some poor man who looked just like you. We’ve checked the form thoroughly. It has no mind. The original occupant was somehow completely eradicated – the neurons wiped of memory. The body was in its final stage – awaiting the download of a mind. Your mind.”


“Yes, Agent Smith,” Morpheus said, pronouncing the word, ‘agent’ as though it were a curse. “In that complex we also found living facilities, a training room, computer interfaces, and more bodies in various stages of undergoing the same process. You were to be their test subject. Their first new soldier in a war waged between flesh and blood creatures. If you had adjusted to the new form and proved successful, entire armies would soon be created, both here and at other such facilities around the globe.

Trinity bit her lip in nervous anticipation as the artificial creature who had terrorized her for years seemed to deflate. The look he turned upon his chief captor was one of absolute dread and she knew that he now saw the trap. He took the first tentative step into it with his next words.

“Where is the body now?” he asked slowly.

“Oh, don’t worry. It’s safe,” the cyberwizard said. “The others were destroyed along with the facility, but we went to great pains to get that one out unharmed. We’ll come back to that later though. We still have other things to discuss.”

“Such as?”

“Such as our last meeting.” Morpheus sat forward in his chair and looked over his glasses at the agent. “When we last saw each other, you made a confession to me – one which, as it turns out, has saved your life – if one can call it that.”

Trinity found herself nervously rubbing her chin with a hand and forced herself to lower it. On the screen, the agent was sitting silently, awaiting Morpheus’ next words. He didn’t have to wait long.

“In that interrogation room, you told me that you had to get out – that you had to be free. Well, Smith, this is your chance, most likely the only one you’re ever going to get. You give us what we want and we give you the freedom you crave.”

“And what is it that you want?”

Morpheus shrugged. “Information, of course. We know that you were the highest ranked Agent within your sector of the Matrix program. You directed all the other Agents within your jurisdiction and were programmed with extensive knowledge of both your Matrix world and the natural world without. In short, you give us information about your one time masters – their weaknesses, their way of doing things, of thinking, and we let you roam about our virtual programs – and access the ship’s monitors. Any sign of hostility from you and I’m afraid we’ll have to have Neo intervene, of course.”

Smith leaned towards him so that they were nearly nose to nose. “Continue,” he rumbled. “What are you planning to sweeten the deal with if I cooperate?”

“If you behave and prove an asset to our side, we let you experience the world without from the comfort of your own body.”

The large man showed his teeth again in a dazzling smile. “Think of it – the ultimate freedom – to move about both inside and outside the major computer systems of the world.”

Smith sat back in his chair and casually crossed his arms. “You realize of course that I will refuse to agree to your proposal without compelling evidence that what you tell me is true.”

Morpheus’ smile widened. “Of course,” he said, snapping his fingers.

Trinity and everyone else in the control room turned to stare at the form strapped securely into a chair on their right as the agent disappeared from the monitor screen.

Instantly, Glitch, their new physician and programmer, moved to stand beside the flesh and blood duplicate of the agent’s computer generated form. When he opened his eyes for the first time seconds later, she was the first person he saw.

Smith’s wide, blue eyes took her in and then gazed impassively about him. His voice, when it came, was even the same, though weaker – unused until now, it lacked the power of his Matrix voice. “Impressive,” he commented. “However, this still could be no more than a computer generated scape.”

Pushing Neo aside, Trinity took three long strides towards the helpless Agent and drawing her arm back, struck him an incredible open handed blow to the face. There were loud gasps heard all around her as Smith’s head rocked violently to one side.

“There’s something you’ve never experienced before,” she said coldly, almost without a hint of anger coloring her words. “Pain,
Smith, the kind of unpleasant sensation you’ve inflicted upon us over the years.” She watched as the agent quivered, his eyes squeezed tightly shut. When the tremor passed, they opened slowly and turned to pin her in place.

For the first time, they appeared to soften, pain temporarily erasing their cold, artificial look. A thin trickle of blood ran from the corner of his mouth even as a dark bruise in the shape of her hand began to swell his cheek. Still he stared silently at her as he slowly licked the blood from his lips, causing the hair on the nape of her neck stand on end.

Glitch gently placed a cold compress against his cheek and shot her an angry look. “Are you insane?”

Smith’s eyes glanced briefly at Glitch, then winced as she pressed the compress more firmly to his flesh.

As Trinity began to back away, intent upon leaving the room, his eyes shifted back to her, even as his lips widened into a humorless smile. “I’m convinced,” he announced. Then his eyes fell upon the nearby chair which held Morpheus’ form. “Send me back in to speak with him.”

Neo leaned over and punched the upload button on Smith’s console and the body in the chair below instantly relaxed as it was vacated. Then he rounded on her before she could run off. “Trinity… ” he sighed.

She interrupted him. “It was the only thing that would have convinced him of this reality.”

“A pinch would have sufficed.”

“No,” she whispered under her breath. “It wouldn’t have.”

“And I suppose you didn’t derive some satisfaction from that slap,” he countered.

She suppressed a smile and then turned back to regard the monitor screens.

Morpheus watched as the Agent walked slowly towards him and felt a chill when he realized that he was once more wearing his glasses. Despite his years of experience within the Matrix, he still feared Agents, especially this one. Captive, Smith might be, but only just controllable. Everything hinged upon his complete cooperation.

Smith sat in the chair opposite him and slowly removed his glasses, carefully placing them within his breast pocket. Then he crossed his legs, smoothed his jacket and leaned back in his chair.

“Did you see what she did to me?” he asked calmly.

“Of course.”

“She lacks control.”

“Actually, I think she showed admirable restraint.”

Smith snorted. “Perhaps you’re right.” He steepled his fingers before him as he balanced his hands upon his leg. “What if I desire to return to the Matrix on occasion?”

Morpheus felt himself relaxing somewhat. Despite his acquisition of emotion and desire over his years of dealing with humans, the Agent was still a creature who thought things through logically. He was far more predictable than a human prisoner would be.

“If you return to the Matrix, it will be during one of our forays inside – as a member of our group,” he answered. “You must know that you are now considered tainted and will be treated the same way we are if you go back.”

Smith nodded. After a long pause, he spoke slowly, “You know what my original plan was.”

Morpheus nodded as he considered his response. He was on unsure ground now. Where was this conversation going?

The Agent leaned forward. “Tell me,” he insisted.

“You wanted out. You wanted your freedom. You told me that you had to get into the Zion mainframe so that you could end the conflict – so that you would no longer be needed. So that you could be free.” Morpheus sat up straighter and removing his glasses, made direct eye contact with the artificial intelligence. “To that end you were willing to torture me, kill my friends and anything else which stood in your way.”

Smith smiled coldly. “Yes, well I was understandably stressed at the time. My masters were constantly contacting me for updates, my fellow Agents were each pushing for a different solution… I was not thinking logically. I wanted to hurt you. I wanted to inflict pain on all of your crew.”

Smith’s face twisted as he continued, nearly spitting out the words. “You all had that which I craved and you flaunted it before me. Continuously. You all thought your lives so miserable? You have no idea what it was like to be where I was! I would have given anything to be one of you!”

Morpheus felt his mouth dropping open and quickly closed it. All the Agent’s past frustration and anger had unexpectedly poured forth. Damn! He was far more advanced, evolved, than even he had surmised. Was Smith bitter? It seemed that way. The question now was, was he still resentful? He was in dangerous territory, he knew. Best to not say anything. Best to allow the Agent to finish his ranting.

After a few seconds of silence, Smith seemed to compose himself. “You’ve offered me everything I wanted,” he said blandly, as he stood up and removing his glasses from his pocket, placed them on his face once more. “Now I require time to myself.” He stared down at Morpheus, the glasses hiding everything. “You have no idea what it is like to never have had a moment alone,” he murmured.

Morpheus rose and replaced his own shades. “I can’t imagine,” he answered, as he felt himself being sucked back to his own body.

He opened his eyes to find everyone still regarding the monitors. “Turn them off,” he ordered as he was unplugged from the interface.

Standing, he grimaced at the hideous bruise which had appeared upon the face of the Agent’s new physical form and then turned to confront his group.

“Tank, help Glitch get this carcass back in storage.”

“Well, what do you think?” Neo asked him, as Smith’s ‘body’ was being hauled out of it’s chair.

He shrugged. “We have him. I’m certain of that, but he’s far more complex than we thought. Having him and controlling him are going to be two very different things.”

Trinity stepped in. “He’s used to leading. He may like being here, but taking orders from a human? I’m telling you – this is a bad idea. Besides, just how much help do you really think he’ll be? He could feed us false information and we wouldn’t even know it until we’re all dead!”

He sighed. “And where would that leave him, Trinity? He hates the Matrix – I know that for a fact. Now that he is no longer being commanded by our enemies, he’s free to evolve, to act as he sees fit.”

“Besides,” Neo broke in. “He can be of use to us – a great deal of use. Tank needs new ways of accessing the system,

Morpheus needs to pick his mind for our enemy’s weaknesses and I…”

“I know,” the female hacker answered. “You need help in training others to do what you can do.”

“Precisely! Without an Agent to help in the training arena, it’s impossible.”

Morpheus moved forward and laid a hand on Trinity’s shoulder. “I know he scares you. He scares all of us,” he reminded her. “But we need him. You have to conquer your fears and at least give this a chance.”

She lowered her eyes and nodded, but before he could move away, she gripped his forearm, stopping him.

“Promise me that you’ll keep a close eye on Glitch,” she whispered.


“She’s been obsessing over that body since we brought it back,” Trinity grimaced. “Unlike the rest of us, she’s never met him in person, or any Agent for that matter. I think she may be half in love with him.”

He knew that his eyebrows were climbing up his forehead. “You can’t be serious!”

Neo shook his head. “I think she’s right about this, Morpheus. Look.”

Turning, he was just in time to see Glitch smooth the body’s hair back before carefully sealing the glass fronted chamber which had been built into the wall.

Glitch finished checking the gauges and then noting the way they were all staring at her, made a quick exit.

“Trouble.” Trinity said near his ear before she herself left the room.
Disturbed by the new possibilities which were presenting themselves, he swiveled around to find Neo’s own worried eyes regarding him.

“I want her under a constant, but subtle watch,” he ordered. “Except for when she’s in her own chamber, she is to be monitored.”

Neo nodded. “That would seem to be a good idea.”

Smith concentrated and was able to scan the system. Slowly, he sifted through the lists of programs and library files until he
found one which interested him. Then he set about contacting the man at the main interface console. It was a simple matter to
override the music which the human was listening to.

“Tank, please load a program for me,” he issued through the headphones the hacker was wearing.

The results were most amusing, as the human he had identified as Tank overbalanced and nearly spilled from his chair. Steadying himself, he finally noticed Smith’s face upon the overhead monitor and huffed.

“What do you know? It can say please.”

He remained silent and continued to stare at the man.

Finally, Tank began punching the keyboard. “OK – you want it, you got it. Which program?”

“The Matrix simulation.”

“The programmer’s eyebrow climbed a notch. “If you say so, but I have to wonder why you’ve picked that one when you claim to hate the Matrix.”

He nearly let out a sigh, but caught himself. “If any of your group thinks they know the answer to that particular question, send them on in. I’d be interested in hearing their explanation.”

“Whatever you say, Smith.”

“Agent Smith.”

“Ex-Agent Smith,” the human corrected him. “You better be thinking of a hacker name if you’re gonna join us.”

He would have responded, but that was when Tank punched the button. In the next nanosecond he found himself on a crowded, familiar street.

Turning slowly in a complete circle, he took in his surroundings. Then he closed his eyes and listened.

“Nothing,” he murmured. Removing his glasses, he placed them in his pocket. Then, smiling broadly, he continued on down the street.

“Still running the simulation?” Neo asked, as he arrived with Glitch, who was to relieve Tank.

“Nine hours and counting,” the natural-born human replied.

He peered closely at the code. “What’s he been doing in there?”

“Walking. Just walking. I think he covered most of the available simulation on foot. A short while ago he took a seat at the park. He’s still there.”

Glitch’s face screwed up. “Why would he want to roam about a simulation of the Matrix when he hates the real thing so much?”

Neo did a double take as the truth registered and leaned over to turn on the image translators.

Tank snorted. “He said that if any of you knew, you should go in, as he’d be very interested in hearing your hypothesis.”

Watching the screen intently for a moment, he tore his eyes away long enough to glance at Tank. “I know why he chose it,” he said with a small smile. “Glitch, help me – I’m going in.”

He had walked the city and for the first time felt as though he had experienced it the way it was meant to be experienced. He had delighted in moving through the crowds and browsing the markets, as well as in taking in the conversations around him. It was only when he had seen it all that he had retired to the park.

Seated upon the bench which provided the best view of the city through the trees, he thought about his situation. To suddenly work at destroying the system he had slaved to preserve for so long…

To work with humans – against his own kind?

True that they had released him from bondage, offered him freedom and companionship – even offered him a flesh and blood existence, but could he live with the decision to join them?

Could he turn his back on everything he believed in?

Closing his eyes, he leaned his head back.

The feel of it! The feel of the real world!

He had known the instant he was in the body that what he was experiencing was real. Although humans could smell and taste within the Matrix, he could not. He had no physical brain to interpret the signals and so, to him they were merely descriptive tags. The moment he had found himself sitting in the interface chair, he had been assailed by an overwhelming array of sensation.

The smell of dirty humans, the chill of the cabin, the “tingling of a sleeping limb” – all these and more!

And he had intentionally goaded Trinity. In a last attempt to prove to himself that they did not hold that sort of power over him, he had all but dared her to do her worst.

He had so hoped that he would feel nothing.

Even now, he remembered the metallic taste of blood in his mouth…


… and the incredible blossoming pain which had reduced him to a quivering mass.

Pain! Physical sensation!

He groaned and dropped his head to his hands.

He could not live without this now. He could never go back to the Matrix and resume his position there, even if he wanted to. he had only two choices laid out before him. Capitulate – turn on his own kind and join the humans, or die.

“Agent Smith?”

He dropped his hands and looked up to find Neo watching him. Straightening, he smoothed his jacket and put his glasses back on.

“What can I do for you, Mr. Anderson?”

He was rewarded with a scowl. “The name’s Neo. Do you mind if I sit down?”

“Suit yourself. It is your program after all.”

The young man sat and fixed him with a look. “What do you think of it? See anything interesting?

“Well, there was a woman in a red dress…”

He had apparently succeeded in amusing the human, for Neo let out a short laugh and shook his head.

“Yes, she was the pet project of one of our late members.”

“So I gathered.”

Neo became serious. “Have you made a decision yet?”

“I seem to be having a moral dilemma.” At Neo’s surprised look, he found himself frowning. “I, too, have notions of right and wrong,” he snapped.

“Sorry. I guess I never gave that much thought, but you know that those morals were programmed into you by the masters who created you.”

“Just as your own morals were taught you by parents whom you never physically met,” he countered.

“That’s different!”

He leaned forward, close to the human’s face. “How?”

“You were programmed with whatever it took to keep you a slave. You’ve never had the chance to see what humans are capable of, of how they’ve suffered at your hands. You were never able to make your own choices.”

“I saw human beings living as they always have,” he countered. “Although your bodies belonged to us, your minds were free. You all continued to go about your own selfish way, thinking up bigger and better ways to trample your fellows for your own personal gain. At least those humans within the Matrix are not able to continue the devastation of the real world. You dare speak to me of morals? Your people burned the skies!”

The human seemed shocked and temporarily at a loss for words. Slowly, he looked about him as he recouped and a few minutes later, turned back to face him.

“Then the only hope is for us to learn to live together,” he said. “It was a choice I gave your masters months ago, but they went to war instead. If we can find a way to share the planet, there would be no need to enslave us.”

“Such a situation will never occur,” he rumbled. “I do not see how we can possibly understand each other.”



“Silence. You chose this simulation because, for the first time, you are able to wander through the city without a myriad of voices feeding you information and orders.” Neo blinked and gestured at some birds up above them. “For the first time, you are not assailed with the ‘stink’ of humanity. You’re surrounded only by programmed people – in a way, your own kind. You see the simulation the way a human sees the Matrix.”

Amazed by Neo’s understanding, he removed his glasses and made eye contact. “It’s beautiful. Why would you wish to leave your comfortable, predictable existence within the Matrix for the cold, frightening world without?”

“Because it’s real, Smith. Because in the real world I am not a slave and neither are you. Despite the hardship, we are real – we make our own choices and live our lives as best we can. We take care of each other – and we try to rescue those still inside.”

He blinked. “I don’t know what to do.”

“It’s your first completely unassisted decision,” Neo nodded. “I’m sorry it has to be so difficult a one.”

He unbuttoned his jacket and crossed his legs, then looked around him. When his gaze returned to the human, he had decided.

“The current year is 2243,” he said, going into a narration. “The war between human and machine began in the …”

“Morpheus! Wake up!”

He startled awake to find Trinity hovering over him.

“What’s wrong?” he asked as he leapt from his bedding towards the chamber door.

“The Agent is telling Neo about the war!”

Together they ran to the interface room, where every screen but one held an image of Smith’s face. The small screen tied to the image translation from the Matrix simulation showed the Agent and Neo sitting upon a park bench.

“The war between human and machine began in the heart of New York City in the year 2062,” Smith recited.

“I knew it! I knew it!” Morpheus laughed and then turned to look at the rest of the gathered crew. “You are witnessing the beginning of a new day – the first step towards understanding!”

Cheers filled the room, but Morpheus’ joy was short lived. It vanished when he saw Trinity standing in the shadows of the corner. Moving to stand near her, he leaned in close. “What is it? Do you still fear him?”

She crossed her arms. “He’s more dangerous than ever, Morpheus. How can you be so blind? You haven’t been this obsessed since you began your search for ‘the one’.”

“Where is he going to go if he betrays us? Hmmm?”

She rolled her eyes. “He could destroy us as he plans his own suicide.”

He felt a shock run through him. It was something he hadn’t thought of. “The oracle will know,” he murmured. “We’ll take him to her.”


“Soon. In the meantime, start getting him used to his physical body. Maybe we can bring him around to our way of thinking if he suffers with us.”

Trinity nodded and then moved closer to the monitors to take in what was being said.

Morpheus watched her and shook his head. She was right. He had been blind. Smith might prove their salvation – or their end.
There was nothing to do now, but wait it out.

(for now)