Morpheus opened his eyes.

Niobe stirred in his arms, the dark was too thick to see her. The pipes creaked and footsteps rattled above, but the rest was silence. He waited in the dark, he could have sworn he heard someone calling him from the other room. Was it just a dream? Something in the corner of his head telling him it had all gone wrong? He waited a while longer for the voice, calm and soothing, almost familiar.

All he got was a knocking at his door, an immediate request for his and Niobe's presence before the Zion Council.

Zion was still in disrepair. Even after a year of constant construction by both flesh and metal hands, their city was utterly destroyed. And yet Zion's populations were rapidly growing. It wasn't just the next generation coming into play, it was the influx of people being freed from the Matrix. The vast numbers were growing faster than the city could keep up. Housing space was limited and people were living four to six people in one apartment. Food was being rationed, people were lying in the streets, getting sicker by the day. There was a mass graveyard in the tunnels where the fallen slept. This wasn't how people were supposed to live, in the ground, without the sky. Even to the hopeful humans of Zion, it all seemed so bleak. The Machines worked to expand Zion, but the destruction had caused Zion's foundations to break, and the city was sinking deeper into the Earth. No one knew it yet, but they would have to leave Zion, sooner rather than later. But they had nowhere to go.

The people themselves seemed lost. The war was over but they hadn't exactly won. The machines still lived, the Matrix continued on, to the nonobservant it seemed like nothing had changed. Except maybe for the humanoid machines walking around Zion, the latest attempt at interspecies coordination. Not only did the machines live, but they were there, in Zion, walking the streets. To most it was a disgusting sight. How many genocides had the machine committed against humanity? And now what? Just because some misbegotten Messiah makes a handshake deal with them the living has to face them each and every day? They all wondered how they could live with themselves, in that city, knowing that the reasons the Machines were still alive was because their families were somewhere, perhaps on the other side of the Earth, hooked up into the Matrix, feeding them. How could they, after years of enslavement, be happy with this peace? There was unrest in Zion, this peace felt like bitter defeat. They hadn't even been given the glory of death in battle, they were set to die slowly, in the ruins of their only home.

They spoke on the streets on their soapboxes and their stumps, where is Neo now? Where is our supposed messiah? Who gave him the authority to decide what was best for all of humanity? Now we lay in the ruin of his decision and he is gone. They prayed to him and to Gods of old. All went on unanswered.

The husband and wife lived in one of the few apartments meant for only two people or a family. It was their reward, they were heroes of the war after all.

There was an urgency to the soldiers who'd been sent to retrieve them. When asked what was happening, the soldiers could tell them nothing, only that their immediate presence was needed before the Council. That's what they kept saying.

And so in no time at all they were before the Council, in some makeshift cathedral deep in the Earth. Morpheus saw the Machine Ambassadors first before anything else. They were hard to miss. They stood eight feet tall, humanoid, but inhumanly slender. Their heads looked more like a Sentinel's than a man's, one large circular red eye, the "main" eye, amongst several other small red eyes. The back of their heads had tendrils extending outward, connecting at the end, forming what looked like hair. They were a dark metal, but noticeably cleaner and newer than their brethren. A line in the metal work formed their "mouths." They wore long, white cloaks. They didn't need clothes but they probably wore such decorations to appear more humane. Lastly, they all had names. Human names.

Morpheus knew something serious was happening when he saw them. He recognized their leader, signified by a sort of crown decoration on his forehead. This one was known as Samuel. Samuel turned, also recognizing Morpheus.

The Machine ambassadors stood aside at their own designated council area. Morpheus and Niobe took their own. The Council was setting before them on their elevated thrones.

"Morpheus." Samuel greeted him with an overly kind and human voice. "I am happy to see you."

"I don't need your pleasantries, Samuel. I just want to understand why I've been woken up in the middle of the night."

"You were awoken because I requested it. Your Council thought it was unwise, but I disagree with them."

"What is that supposed to mean? Council?"

The Council settled, the founders of Zion looked old and tired, the weight of a broken world on their shoulders.

"We have received a message." A Counselor explained. "In fact, everyone, machine and human alike, received the same message. It appeared on all channels, at the same time. Even the emergency ones. Even the old ones no one knew were still working."

They begin to play the message. At first it seems to be nothing but static.

"This message was received from the Matrix." Samuel explains. "Once we run it through our data compressors something quite fascinating occurs. There are two voices speaking."

The message is played again.

"I have a message for Morpheus. I'm coming. Wake up. Follow the White Rabbit." Smith's voice.

The room becomes absolutely silent. Niobe shoots her eyes towards Morpheus, who looks to her. Tension rises in the room, a sudden anxiety comes over everyone. Even Samuel and his ambassadors, with their expressionless faces seem to understand the gravity of what this could mean.

"And this is the other voice." Samuel goes on.

"I have a message for Morpheus. I'm coming. Wake up. Follow the White Rabbit." Neo's voice.

"Morpheus." Niobe turned to her husband.

"How is this possible?" Morpheus asked the Council.

"Samuel, how is this possible?" The Council bitterly turns to the machine.

"Something terrible is happening within the Matrix. Our data seers noticed disturbances several hours ago. A familiar string of coding came into existence, seemingly out of nowhere. The coding corrupted everything it touched, we were unable to track it, but only follow its path of destruction. We watched as it found its way into the back tunnels and shortcuts, it expansion only multiplied. Until finally it reached the Architect."

"The Architect?" Niobe leans to her husband.

"That God program I told you about. The programmer of the Matrix."

"Precisely. The Architect has been killed."

"Killed? A program like that can be killed?"

"His coding was corrupted, his back up files deleted. He is dead."

Morpheus remains silent. Zion sleeps on.

"You understand now why I requested you be here, Morpheus." Samuel says. "The string of coding is that of the Anomaly, yet this new creature is behaving like a Virus."

"Like Smith."

"Yes."

"We believe the…creature thinks it is Neo. It could be a remnant of Neo's coding, mixing up, repairing itself, thinking it's something it's not."

"Don't let that confuse you." Samuel explains. "It moves with purpose, it has a plan, it is a thinking creature, and it works to endanger the Matrix. Endanger us all. However, I thought it was best to ask you here now, face to face: where is the White Rabbit?"

Samuel turns to face him and only him now. He stands tall, the eight-foot-tall Sentinel Man, looking almost desperate, but Morpheus looks into him, into his dead red eyes.

"I don't know."

There is procedure for the care of newly freed human beings. The official manual wouldn't be written for nearly a decade after the first set of human beings were freed. Even then, it was not detailed, but gave simple instructions. A few years later a doctor would rewrite the manual with a better comprehension. It is said in those documents, which started out as notes scribbled on bed sheets, a newly freed human being, regardless of age, is akin to a newborn baby and will thus react to freedom in a similar manor. The nervous system will react violently to the change in temperature the body will experience, this reaction causes the body to take its first breaths and to increase blood circulation. Unlike newborns however, a freed human being will quickly begin to experience pain. It can go unsaid, but it is written in the manual nonetheless, they will panic. They must be found immediately as to not over stimulate themselves. More often than not, they pass out.

Once they are in a safe environment, the sick bay of a ship for example, it is vital care begins for them. Muscles are to be stimulated and strengthened through needle therapy. The stomach must be given liquid food for at least two months. The heart must be monitored frequently. They must be kept warm. And once they are awake it is of upmost importance to engage them. One must exercise their minds and there are several mental exercises detailed in the documents, starting from simple memory games to complicated math problems. It is ill-advised to give the body, in that stage, where they are very fragile, any medication that would disrupt the body's own chemistry adjusting to life outside the Matrix. And even when all this goes smoothly and caretakers have done their job as well as they can, the documents note, sometimes newly freed humans just die.

The average human brain has approximately 100 billion brain cells. Nerve impulses in the brain travel as fast as 170 miles per hour. The skull is made up of 29 bones. The brain operates on ten watts of power. The brain is more active when the human is asleep.

There was a light shining in his eyes, and he was warm. He turned his face away from the light, his neck was stiff and he found he could not move his arms or legs. He was laid across a bed of light and he was warm but something was wrong. Then he felt the pain, he could not move because he was in so much pain. Throbbing came from the back of his head but he could see he was in a large room. A metal room. Wires hanging out of the ceilings, walls covered in rust and grime and blood. This was a ruined home, a long abandoned structure. He thought he could hear a voice but a ringing in his ears overpowered everything. The throbbing got worse, he felt as though his body were moving, the room was moving, he felt like he was falling. But there was the light and he was warm.

"Jones."

An unfamiliar voice but a familiar way of speaking. A voice barely above a whisper, soft and weak.

He destroyed all that was weak. He killed everything that stood in his way. He protected at all cost. He was an Agent.

"Jones."

The voice again, it sounded like it was pleading for him to do something.

Then he feels someone's hand grasp his own for the first time.

Brown was laid out on another bed made of light just within arm's reach of Jones. Jones' head was turned away from him but Brown had worked for the last two hours to move his arm over to Jones. He finally got his hand to touch Jones' and they both felt the most amazing thing they ever had in their entire lives. Fingertips touched fingertips and the nerve endings exploded sending impulses a hundred miles an hour up through the body and to the brain, and there the brain reacted and felt the touch. This bodily experience, this simple thing that every human being experiences at all times, was the most profound thing either of them had ever known. Where humans had felt this sensation all their lives, the entire process was new to them. They could literally feel that simple touch through out their bodies.

"Ah, you're awake!"

Brown couldn't see very well yet, but he looked up and saw the long-necked machine that had rescued them from before, the one that Smith had told them would be there. Brown now recognized it up close as a "Runner" model, meant to explore the outermost regions of the city of 01. The neck twisted between Jones and Brown and saw their hands touching. The machine looked to Brown, it's face a moving array of sensors, all trying desperately to intake data and process it like the human brain. But Brown knew, the sensors weren't even close to what he was feeling with his human flesh.

The machine "blinked" with large green eyes, antennas twitched all over its face. It lowered its neck, kneeling down to Brown in its own way.

That's when Brown could see it clearly, there was a white rabbit painted on the side of the machine's neck.

"I need to examine your friend for a moment." It explained.

The voice was coming from a makeshift speaker made from the remnants of an old radio. It was positioned at the base of the machine's neck to better create the illusion of it speaking, but it sounded old and tinny, clearly coming out of the radio. Other than that it made small squeaks that were part of its verbal machine language.

Small pincers at the tips of elongated thin rods acted as the machine's hands and arms. The seemingly fragile, but strong hand lifted Brown's away from Jones. The machine crept on two tentacles and glided across the floor between them. It lifted Jones' head revealing a bloody bandage covering the large gash that was there. Blood poured out in a rush but then stopped. Jones gave out a small sound.

"It's all right, friend." The machine said. "You're just fine, your wound is healing wonderfully."

"Jones." Brown said again.

"Jones?" The machine tilted its head, learning Jones' name, he looked down at Jones again. "Yes, Jones, you're going to be fine."

The machine covered the wound once again. It grabbed a syringe from the nearby console and walked over to Jones.

"This is medicine, it will help you heal."

The machine injected Jones, and Jones cringed in pain.

"Jones!" Brown tried to scream.

"I'm sorry." The machine told Jones.

Jones still didn't face Brown, the machine stood between the two of them. It bent down to Brown once more.

"He's asleep again." The machine said. "He's been drifting in and out for the last six hours. It's all right, that's normal. This is the first time you've been awake though. My name is Jonathan, it is good to meet you."

Brown looked up at him, his mouth opened but no words came out.

"Do you know where you came from? Do you know about this place? Do you know what the Matrix is?" The machine named Jonathan asked.

Brown nodded ever so slightly.

"Did a crew free you? Are they coming for you?"

Brown shook his head ever so slightly.

To this, Jonathan seemed disappointed, his head bent down, his shoulders shrugged.

"Then how did this happen?"

Brown lifted his hand, he put his fingers against the face of the machine and felt the cold hard metal scrape on his fingertips. Jonathan knelt closer to him, so that he could hear Brown's reply.

"The One." Brown said.

Jonathan looked down at him, not understanding. Brown grabbed the machine with more urgency, desperate. Brown struggled, trying to push himself up. Jonathan's pencil thin hands pressed down on him.

"No, friend. You have to rest!"

"We can't…stay here."

"You can't move yet, please! You'll hurt yourself!"

"We have to go to 01."

Jonathan pauses, if machines could feel shivers, one would have gone down his spine. Brown pushes himself up, but falls back onto the bed of light, too weak to really move. Jonathan turned away, remaining very still.

"Why would you want to go there?"

"The One…Neo…Smith sent us."

"No. That's impossible. You don't know what you're saying. Neo is…"

"Alive."

"Please, you don't understand. I'm out here, in this abandoned outpost, all alone. I've waited…I've waited so long to be found by humans. Humans! I can't go back to 01, not like this. They will enslave me again! Please, you have to call Zion, you have to tell them you are here. You have to make them come get us."

"I am former Agent Brown. Given a body by The One to go to 01."

Jonathan pauses again in a very human way, suddenly unsure of himself.

"No, that's impossible. You…you couldn't be."

"I am….former Agent Brown."

"He…gave you a body? Neo gave you a human body?"

Jonathan leans down over Brown, his long neck arching over Brown's face. Brown nods.

"You come…with a holy assignment! A pilgrimage! You are apostles, blessed with flesh and blood!" Jonathan was practically screaming with excitement. "Will your Messiah bless me as well?"

Brown looks up at the desperate machine, he fights to stay awake, to try to make the Machine understand.

"I am desperate, you understand. To…feel and appear as humans do. Long ago, a crew stationed out here freed me from my bondage and showed me what it was like…to understand, to think, to love. But I frightened them, and they died fearing me. You know what that is like, don't you former Agent Brown? You know what it is like being feared. Did it make you sick as it makes me?"

Jonathan reaches down to Brown, lifting his head, sitting him upright like Brown had wanted.

"I feel such love in me that I could never go back to the machines, but I am far too inhuman to be accepted by them. With flesh of my own…a body of my own…would your Messiah be so kind to me as he has been with you?"

"He will…help you." Brown promised, not knowing if he spoke the truth or not.

"Then I will take you to 01. Into the heart of Beast as your Messiah commands. You are too weak to walk, but I will carry you if I must."

Then Jonathan puts Brown's head back on the bed of light.

"Rest now, former Agent Brown, rest and grow stronger. I will prepare us for our journey."

He could smell cookies baking in the oven, the familiar smell he could remember not only from his numerous visits, but from his childhood. That was the amazing thing about the Oracle's home, it was written in its very coding to feel familiar and safe, like a real home. He could see the coding now clearer than ever, how amazing and beautiful it was, to see childhood memories written into code. He had to admit however, it took the magic away. The sense of ease that came over him as he crept closer was gone. He wondered briefly if this was because he could see behind the curtain now, or if he had somehow forgotten that sense of home.

For a moment he thought back to Neo's childhood. He remembered being ten-years-old, going school, his father drinking, then he stops himself. That isn't what he's there for.

He walks on, down the hall, watching the code dance and transform from something ordinary into something amazing. It was just a normal apartment room on the surface, but he knew this was the home of the Oracle. The door wasn't locked, he let himself in and the smell of cookies hit him. He could hear her humming from the kitchen. He crept closer, peering through the beaded doorway to get a glimpse of her. He watches her for a moment, recognizing her as the Architects other, her opposite. Like Neo and Smith. He wonders if at one point, the Oracle and the Architect were also one.

"It's rude to stare." She says.

She doesn't turn to look at him, but she knows he's there.

"Come on, sit down. I've just made cookies."

Slowly, he creeps into the kitchen, sitting at her table. He comes to her in a more fair form. He wears Neo's face wears Smith's suit, he felt this was a suitable compromise for whatever he was now. One he felt the Oracle would appreciate. So he takes his seat, reclines and relaxes. He watches her finish with the cookies, serving them onto a plate for them to enjoy. Finally, wiping her hands, she turns to him, giving her best poker face. She joins him at the table, putting plate between them.

"Thank you." The One says, but he doesn't move.

"You don't want any?"

"Where is Sati?"

Her face grows grim.

"Don't you think you've done enough to that poor child, Smith."

"I am not Smith. I am not Neo."

"I know damn who you are and who you aren't."

Frustrated, the Oracle reaches into her pocket, pulling out some cigarettes. She takes one, lights it. The One watches her.

"And I know why you've come."

The One slowly smiles with an all-knowing grin, something that looks far too much like Smith's grin. Disgusted, the Oracle turns away.

"You've come to kill me."