Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.
Caveat: If anyone has read my Beetlejuice fan fiction they know I am the queen of super short chapters. I apologize for this, but such is the nature of my muse. She makes me break things up in a certain way and I must obey her.
Synopsis: If you haven't read my other two Matrix works, In The Beginning and A Tangled Web, you're going to want to read those before starting in on this. It's been three years since the end of A Tangled Web, and Christopher is indeed caught in a tangled web. He's continuing to work toward freeing humans from the machine energy collectors, but a faction within the human city of Zion is plotting his death and war with the Machine city Zero One is about to break out. The Architect is angry that so many humans have been freed, thus creating the beginning of an energy crisis in Zero One. Even his control, in the form of the legend of The One, is beginning to erode in the face of mass escapes. Everything is coming to a head, and the destiny of the human race might not actually rest in Christopher's hands.
In three year's time, Christopher rescued over three hundred people from the Matrix. These people, grateful for their freedom and eager to work against Zero One, devoted themselves to helping Zion in any way they could. Through their "life experiences" in the Matrix they brought varied talents and skills. There were some great difficulties at first. Christopher found the older the mind, the less likely for a clean break. Several freed men and women suffered psychotic episodes after being unplugged. Eventually, the council made a law that no human could be removed from the Matrix after the age of eighteen. Christopher, personally, tried to stick to the fifteen to eighteen age range: old enough to contribute to society but young enough to live easily without the Matrix.
The engineers designed a new, more efficient and maneuverable hovercraft. Within two years they had five of these ships built: the Mjolnir (nicknamed the Hammer), Icharus, Polaris, Vigilant, and Caduceus. The engineers had also built on Christopher's skull probe apparatus and perfected it: each of the new ships came equipped with seven of them and a monitoring station.
Christopher had developed a system of monitoring equipment so that while someone was connected to the Matrix, another crewmember (called an "operator") could keep an eye on them. The system sported seventeen monitors: three displayed code for the Matrix, seven displayed vitals for the crew connected to the Mainframe. The other seven were an upload link to the crew's minds. On these seven monitors, the operator could see their position in the Matrix, direct them to the nearest exit location, and upload any information they may need directly into their brain. The operator was responsible for keeping the crew relatively safe while they were connected to the Matrix, as well as uploading and downloading them to and from the Mainframe.
As Christopher and the rescue teams saved more and more people from the Matrix, the agents started finding them faster and faster. The rescue teams abandoned many rescues because their half hour time limit became simply not enough time. Rather that try to lengthen the time limit, Christopher had instead come up with a system of upload and download using what he called "hard lines" into the Matrix. The operator would upload the rescue team into an area where a hard line existed, the team would find and retrieve their quarry, and the operator would guide them to the nearest hard line to exit the Matrix. Using this method, rescues were achieved faster and abandoning a rescue was no longer necessary.
Martin had immediately proved himself to be an asset to Zion. He was not afraid of working, and took to his new life with the ease of a child. His mind had no trouble coming to terms with the reality he was presented with after his recovery was over. After only two nights with Christopher, rescuing others from the Matrix, Martin had seen needs that even Christopher hadn't anticipated. Martin had set to work creating a Construct program...a program separate from the Matrix mainframe where they could load things they needed such as weapons, training simulations, and the like. Christopher found himself energized by his teenaged companion and set to work creating programs to compliment their new "loading platform."
Somehow, in the middle of almost nightly rescue missions and endless software programming, Christopher and Miranda had conceived and birthed a Daughter. Her name was Maria. She could invariably be found on the hip of Christopher or Miranda, or any of the other crew of the Osiris. As she grew, she came to regard the ship as her home, the crew her extended family.
Christopher had garnered the respect of Zion...with one or two exceptions. Reinette of the Elder Council and her lover Stephen (captain of the Nebuchadnezzar) had not been able to gain support for their covert plan to kill Christopher. Their only ally was Michael, another sitting member of the Council. Marlin, who had sided with Stephen against Christopher initially, had been won over by Martin's accomplishments.
The machine city had, until this time, turned a blind eye to the human settlement of Zion. The sentient program responsible for maintaining the Matrix ("The Architect") needed somewhere to put the humans not suitable for harvesting, and so the machines left Zion alone. With Christopher's activities they had been forced to look again at the humans and decide what was to be done with them. Alarmingly, more and more humans each year were being smuggled out of the energy collectors, and the cloning farms were beginning to have difficulties keeping up with the losses. Therefore the machines had begun posting patrols in the places where the humans were likely to hide while hacking into the Matrix. There had been a few minor skirmishes, always ending in machine failure due to the Electromagnetic Pulse bombs the humans armed themselves with. These EMP bombs would completely disable anything mechanical within a ten meter radius.
Meanwhile within the Matrix, despite the Architect's upgrades the agent programs proved unable to stop Christopher and his cohorts. The Architect's frustration grew. He knew he would not be able to completely stop Christopher...indeed, he wanted the very opposite...but he had hoped to keep the loss to the energy collectors to a minimum. As it stood, at the rate the escapes were increasing, the machines would simply not have enough humans to replace the escapees. They had already increased clone production, but the fact was growing a viable, usable clone took time. If trends continued, they would eventually not be able to grow clones fast enough to meet demand.
The world turned. Life continued on despite the trials it faced every day. After all, there was work to be done.