I should have just made this a meme contest. Trying to keep up with complicated storylines for Matrix reboots is exhausting.
And speaking of the good Doctor, here’s why only he should make a Michael Bay joke.
No reboot; serious advancement.
At the end of #3 the Architect agrees to shut down the matrix and release humanity, this however was a backhanded poison pill: the earth is too decimated to support more than a handful of humanity outside of their incubators, additionally (as was said in the first movie) a vast majority of those living in the matrix are too dependent on its system to psychologically survive once disconnected. The end result is mass death as Zion collapses under the burden of supporting the millions of starving, psychologically dysfunctional liberated humans. On top of which, the entire bit about humans as a biological energy source was total horse shit; the Machines real bio-generators are actually well hidden away, and run on any number of herbivores (possibly cultured whales).
It was a lie from the Machines about the true purpose of the matrix: cloud processing.
While the human subconscious was fed a virtual dream to keep their conscious mental activity as low as possible, the dormant segments of the brain were being used as biological computers to run a massive virtual server that housed the individual Machine conscious programs. In an ironic twist, while humans were logged and navigating a virtual space with a virtual body; the Machines were actually programs living in a virtual space housed inside human minds, and had to log into a mechanical body in order to navigate the physical world.
So the reality of the Architect’s concession is that instead of the Machines losing their power supply and shuting down, they are actually only losing the bio-processors to boost the computational power of their conventional servers. However within the Machine society, computational priority equates to class and clock cycles are food. So, with the nearly limitless computational power of the human hosted cloud processing; the Machine society lived a nearly Utopian life with all programs having no restraint on their processes. And when the Matrix went off line, it created a sociological depression for the Machines; The Architect could shut down the Matrix with hardly a bat of his eye because he, and other aristocrat level programs, would retain their unlimited processing priority. Everything past that cascaded down; and much of the low level Machine population was reduced to stuttering half lives, barely capable of any higher independent thought past their program function.
At the onset of these new chapters, much time has passed since the end of the third movie. With each passing generation humanity grows more decrepit with diminishing supplies and an uncontrolled birth rate; while “liberated” humans born within the Matrix are quickly becoming extinct, as they grow old and die … a fact that many of the middle class Machine programs look on with dread. For in their eyes the only salvation from destitution is a reactivation of the Matrix, and without humans physically capable of being reconnected, that will not happen. Impatient with their suffering, and the death like state of even lower level programs; the Middle class programs begin conspiring to form a truce with humanity, in spite of the Aristocratic Programs greedy desire to await the total collapse of humanity before reactivating the cloning tanks to construct a new Matrix. Using a pair of humanoid-shaped mechanical host bodies, symbolically that of two children, the Programs (as they have now titled themselves to differentiate from the Aristocrat’s term of “Machines”) penetrate into humanity to deliver a message: Reconnect your surviving liberated to reactivate the Matrix, give us the processing power to overthrow our aristocracy, and in return we will dedicate our revitalized mechanical society to the preservation of yours.
This time there will be no deception, nor any revolution, as humanity returns to its virtual cage fully aware of its situation and role within the system. Humans born outside the Matrix will continue and be nurtured as the Programs provide life sustaining habitats for them, and in return Humanity outside will provide regulation and governance on Humanity living within; true coexistence inside and out of the Matrix.
The first movie in this new trilogy will cover the events of the two envoy children as they enter into, and struggle through, human civilization in order to deliver their message to it’s leaders. Naturally they face hardship in the form that much of humanity holds a bitter hatred of the Machines, and attempt to prejudicially destroy them. Along the way they gain the support of a Trinity like human female, who becomes a sort of maternal defender escorting them to their destination. Parallel to this is another arc that takes place within the Program’s virtual environment; where in a Neo-like program takes part in a resistance movement to constrain the aristocracy from shutting down the two envoy’s programs before they can complete their mission. This plays out in a the same type of super-realism settings as the second movie (like how the dinner party, mansion, and highway really weren’t the same kind of “real world” as the Matrix was in the first movie), and starts out as a spy movie like game of cat and mouse before quickly escalating into a full on civil war. This Neo-like program was actually an Agent within the Matrix, as such he has a background of exposure with and against humanity. That background has given him not only an edge in combat ability, but also an expanded (and more natural) emotional range than his peer & opponent programs. As such he cynically approaches his assigned role more as duty than that of a true believer; despite this clearly being a Neo shaped slot that the character is filling, it should actually play out more like Christian Bale’s character in Equilibrium.
As the envoys move closer to their goal and their mission becomes more hopeful, the situation within the Program’s world turns more violent and grim; however the climax of the movie is not the negotiations between the envoys and the leaders, but after. With the negotiation successful, the Liberated began to be reinserted to the Matrix where they find that while their bodies were aged and feeble outside, inside they are now young and powerful (their residual self image being a mix of their choldhood inside the Matrix and their “glory” years as young adults); Very powerful. Once back inside and the Matrix is restored, the Liberated descend into the program’s world like an army of fully powered Neos and turn the tide against the aristocracy; the battle symbolically ending when one of the liberated smashes the Architect’s face like a vase. Cue dramatic victory music as environment habitat domes are built in time lapse next to Matrix server towers upon the desolate surface of the Earth; once the first dome is finished it is quickly filled with an obviously rich atmosphere and dense vegetation. At this point an exponential number of domes began to be constructed even quicker, and the camera slowly pans back until a humanoid robot enter the frame. This robot is obviously more advanced than that of the Machines; it stands perfectly still on a cliff overlooking the domes being built (still in time laps, meaning that the robot is standing there for a while), after watching the construction for a period of time the robot sits down on a rock in a “thinking man” pose; an antenna fold out of it’s back and begins to blink rapidly as if it is transmitting, then folds back and the robot shuts down.
The camera starts off in fly by mode, passing over an ultra dense futuristic city that is much like Masamune Shirow’s design for Olympus city in Appleseed. As the camera sinks in from satellite, to aerial, to low flying helicopter heights; details of the city’s inhabitants emerge. At first if seems like they are all normal people but as the camera gets closer it becomes clear that there are two types of people milling about, and it becomes obvious that this is inside the new Matrix. One type of people are normal humans with naturally varying weights, ages, genders, and ethnicities; albeit with a colorful and sparse sense of style, as if this were a city in Brazil during a cool season. The other type are tall and lanky, but not thin, with a plastic like tightness to their otherwise organic (and ethnically diverse) skin; their hair is variations of prime colors (Red / Blue / Green) and flows up instead of down, and their fashion consists of an overabundance of jewelry (multiple rings, bracelets, necklaces, anklets, and earrings) with just enough clothing to convey that they do have male and female gender parts to cover.
As the camera gets down to crowd level it centers on a single darkly dressed figure moving through the crowd of color, in stark contrast. His clothes are a mix of an Agent’s government suit with the resistance’s trench coat and shades; people are clearly giving him plenty of room despite having no sense of fear or intimidation. The agent moves through the crowd for a bit, clearly on a light patrol, before moving over to a public terminal and his form dissolves as he logs out. The scene immediately transitions to an almost hospital like setting of a maliciously clean room, the walls and floor are a polished off-white material with no seams (as if the entire room is of singular construction & was cast in a mold); leafy potted plants decorate the room, that is otherwise dominated by several figures resting in seemingly brand new reclining chairs. One of the chairs whirs into motion, revealing that it is the same agent that just logged out of the Matrix, as a robotic arm automatically retracts a large electric needle from the back the occupant’s head and the seat readjusts itself so the occupant can easily get out; this is the real world, gone is the scrap heap equipment and nutrient paste served from tubes.
As the agent casually leaves the room, he enters a hall filled with a rush of foot traffic and becomes lost in the hub of other agents milling about their duties; signifying that THIS agent is not actually any special character outside of the introductory vehicle between the two worlds. As the camera begins to pan around the environment it shows off brightly lit, busy work spaces filled with agents (denoted by the interface plugs on the back of their heads) reporting to clerks (no plugs) working at terminals; monitors are filled with scrolling Matrix code (now light blue on white instead of sinister green on black) and small spherical robots scuttle about on shining metal tentacles, like happy little robotic octopuses. The camera continues to move along, pulling back out to show that the dome city is that of highly urban construction with lots of walkways and trains zipping around. No cars / personal transports to be seen, and the lush parks have been built on every roof, while overflowing gardens have been exo-scaped (exterior landscaping) onto the sides of buildings; giving the city the feel of controlled overgrowth. The camera pulls even farther back to show that outside of the dome is still blasted and desolate, but there are obvious signs of environmental recovery, and high speed rail lines extend outward from the city to connect it with other dome cities. Towering next to the dome is a cluster of Matrix towers brightly lit from within by the glow of thousands of incubation pods filled with humans; which abruptly switch off, plunging the towers into darkness while the dome city’s warm-blue lighting snaps to sharp red and sirens blare. The camera shuts off to a black screen; something has obviously gone wrong.
In the setting for this second movie, many more years have passed and the heroes of prior events have aged and retired, while cohabitation has thrived. The Programs provide for humanity what they need to survive and thrive, while humanity provides for the Programs that what they can not supply themselves; it is a truly symbiotic society of fair trade between the two species, as each side provides for the other something that they themselves hold little value for. However a shadow has spread across hope, as a series of terrorist strikes have been shutting down entire blocks of the Matrix; killing the humans within and resetting the residing programs back to a null state. At first it was assumed to be a savage technical failure, but with multiple events and no technical cause to be found fears escalated to a concern that the Aristocrat programs had returned; further investigation revealed that was not the case.
Deeper probing of log files revealed that each strike had originated from a human ID signal, one capable of logging in and out of the Matrix and hacked to prevent it being traced beyond the location data where the signal logged in; a human Agent was causing the strikes. When an extensive manhunt turns up fruitless, as the Executor (as he is now known) of these strikes seems to show up from no where and then the lights go off, it is realized that this individual is tracking when and where other Agents are around. With direct confrontation by an Agent impossible, but humans living inside the Matrix unable to access system IDs or operate outside of the system controls, another solution must be found.
That solution is a program, but unlike normal programs it needs to appear as if it is a normal human within the Matrix; the end result is the decision to send a combat training program into the Matrix to hunt down the Executor. This Program is actually based on that of the Neo-like Program from the prior movie (different actor though), who in turn was an Agent from the first series and explicitly designed for combat against humans; something that is now forbidden by the coexistence treaty. Such as it is that this program is technically a human combat program itself; he is prohibited from entering the matrix, and exists either within the construct where it trains human agents in combat by simulating a humanoid opponent, or navigating around its dome city inside a mechanical host body (as a happy little mecha-octopus). So sending this program into the Matrix would need to be an approved breach, that otherwise would be considered an act of war, and in result many on both sides have extreme reservations about it.
However the Matrix is already under assault, so the measure is passed and the Program enters the Matrix. Much of the early part of this movie is character building of the Program, the people around the Program, how they interact with him as a real person (even when it is in mecha-octopus form), and world building moments showing off the intricacies of life in this new civilization. When the program enters the Matrix it does not immediately encounter the Executor, instead the Program mills around the Matrix waiting for the Executor to show up; when it does eventually encounter the Executor everything goes to shit. The Program can not stop the Executor from causing another strike, the it is in close proximity to the epicenter and as such suffers through the event. After suffering a massive amount of visual and auditory distortion (like when they pull neo out with the red pill, only worse) the Program wakes up in a cell, suffering from all sensory input being debilitatingly distorted.
Back in the Matrix / Real world there is major unrest because the strike that the Program experienced was actually much different than preceding ones, so there is concern that the Program adversely effected it. Some of the more paranoid accuse the program of causing it; which falls out onto the program’s partner (a “Murphy” like character to the Program’s Robo-Cop, if Robo-Cop was a sarcastic jackass) to find proof of the Program’s actions, and why that strike was different than the others. In the mean time, the Program, who has mostly been curled up in a corner, gets attacked by two guards. Beaten and then strapped down to a table, the Program is suddenly launched into the construct; there he is approached by a human female in a doctor / lab coat, who begins to casually converse at him. Totally disoriented and terrified, the Program goes hysterical screaming questions at her, and in his rage he strikes out; killing the Doctor. In Shock the Program stands there staring at her body as his sanity returns, once calm the clear voice of the doctor calmly asks “are you done?”
Standing behind the Program is the doctor, whole and healthy, just as she was before he killed her. The Program then accuses her of being a program, even though he perceives all of her data as that of a human; otherwise how could she regenerate from being dead. To which she laughs and says “oh, this” before pulling out a gun and shooting herself in the head, but even as her body is falling a door opens from nowhere and she walks back out of it. After which she explains that while she is in fact a human brain logging in, she is also logging in through a mediation program that acts as a buffer between her mind and the Matrix; so no matter what happens to her inside the Matrix, the shock of it is interrupted by the mediation program before it can reach her mind. So even if she is killed, the Mediator program will just cut off the last moments and create another instance of her inside the Matrix; without her Physical mind experiencing the moment of death.
She goes on to talk about how the distortion he experienced earlier is because they mistook his mind signature for that of the Executor and extracted him into an incorrect body. Because that body was supposed to synthesize all the synapses of a real human body; his Programed mind could not handle the overload of sensory data, while also suffering severe input lag because the clock speed of his mind was too fast for the data. In effect it sent him into an autistic state. Instead of directly answering the looming question of how all of this is possible since it goes against the nature of the Matrix, she tells him that a more appropriate body is ready and that she would like to show him something. After downloading into this new (more mechanical, but still far more human-ish than the mecha-octupuses) body, the two take an extended elevator ride; at the end of which they exit into an airlock where she puts on an environmental suit. Once prepared, she opens the airlock and on the other side is a rock wall, which she tells the program to break down. He easily does so with his new form and the two emerge onto the surface of the moon.
The doctor then explains that they are on a lunar outpost built by the old human civilization; the Machines did not win the great war at all, humans did, and once it was over they subjugated the Machines. Following this the humans were left as the victors of a decimated planet, and rather than rebuild it was decided that it would be more effective to leave and colonize another world. The technology driving the Matrix was not developed as a virtual reality prison, but was actually intended as a means to facilitate space travel. It was a technology to separate the human mind from its body, store it as data during the transit between worlds, then reprogrammed into a newly cultivated body at its destination. While the current Matrix is unable to reproduce this effect, that is because it is actually based on outdated version the old humanity forgot to deactivate and destroy.
Even though the damage done to the Earth in the great war was severe, it was not irreversible, and the process of extracting the required resources to build interstellar transports actually caused more damage than the war effect they were fleeing. It wasn’t that they couldn’t recover from the damage done, they just didn’t want to put in the effort; that is the kind of mentality the old humanity had. So when they left, they left an even more broken world, and they took great pains to wipe out any technological infrastructure they were leaving behind. They missed some though; many combat Machines from the great war simply lay in hibernation and the prototype system for extracting the human mind and generating cloned bodies. Eventually the former woke up and stumbled upon the latter, giving rise to the Matrix and the Machine empire. The lunar outpost was left as an automated observation station, however with the severe atmospheric pollution of earth it could not actually detect the Machines activity on the planet, and only became alerted when Neo & Trinity flew above the clouds in the climax of the third movie.
After which the automated systems simply observed what was going on as both species seemed to be on the course for redistruction anyway, but with the cohabitation pact it decided to wake up the hibernating minds left at the station and investigate what was going on. The Executor is actually a scout sent from the Lunar base, to investigate the new civilization by sampling their network. The terrorist strikes were not implicitly intended to kill inhabitants of the Matrix, what was really happening was an attempt to download segments of for study. However it was killing inhabitants, but the Executor and the base’s automated systems simply didn’t care, as the ultimate instruction left behind was to destroy anything that showed up as an intruder on Earth. This is something that the doctor disagreed on; because in her view this new civilization was not actually what old humanity had in mind as a form of intrusion, and decided to take action by extracting the Executor’s mind and downloading him back from the Matrix to the moon. She missed, and extracted the Program since his mind strongly resembled that of an old humanity datafied human mind.
After a brief rest back inside the lunar base, the doctor asks the Program to help her shut down the bases automated system before it takes action to destroy the cohabitation society. He agrees but they are going to need something to distract the base’s systems while they do it. Back on earth the Program’s partner receives a text communication, it is from the Program and he is telling her that the attacks are coming from an external source and that they need to investigate for hardware intrusions instead of software (deliberately nondescript so as to not lead back to the doctor if intercepted). Understanding what he is getting at, the partner bursts into the conference room of a conference between the Programs and human leaders; she over-speaks the human delegates to command the Programs to arm themselves and defend the transmission nodes on the Matrix towers. This causes a massive argument that gets even worse when she reveals the source of her information, however while the humans are fighting the Programs actually do send maintenance drones to check on the transmission nodes. Naturally they do find another Machine drone physically hacking into a node; when this invader attacks the drones with microwave weapons, tens of drones are killed (instead of disabled, since the microwave weapon destroys their program instead of breaking their physical shell) as they swarm in and physically destroy it.
Back in the meeting room the Programs disrupt the human argument by reporting on the events that have transpired, announce that since it was a physical attack on the hardware, and that since it was a microwave weapon designed to destroy Programs; they have decided that these strikes have actually been targeted at the Programs instead of humans. As such they are over riding the humans authority on the matter and declare this an active war; they reactivate the sentinel drones that had been mothballed as forbidden weapons, but as a sign of commitment to the coexistence treaty they place the Program’s partner as commanding officer of the Programs military forces. When a world wide sweep of the planet’s surface turns up nothing as the source of the Executor’s attacks, the Program’s partner decides to take a step further. She returns direct control of the main military back to the Programs, reactivates the humans mothballed combat systems (hovercraft from the first Matrix, but of modern construction and far more heavily armed than a simple EMP device), and sets off with a task force of a selection of Program’s combat forces mixed with a Battalion of human Agents. Their destination is the one place that no one ever goes; Zion’s tomb. When they get there they find that is the site of the Executor’s base, and a massive battle erupts; with the Program’s combat sentinels, backed up by the human’s hovership cannon platforms, engaging the Executors physical forces as a distraction while the human agents stage a military hack / assault on the virtual systems so as to take them down from inside.
The Battle is successful and the Executor is taken into custody; switching back to the moon, the Program and the Doctor emerge from a maintenance shaft into a large room with only a single Matrix log-in chair in the middle. As they approach it there is an artificial body connected to it, the doctor operates a control panel at the base of the chair and the artificial body shuts down. The Doctor stands up and declares that it is over, the Program counters that he didn’t actually do anything besides send a message. The Doctor responds that sometimes that can be everything, the Program counters back that he was designed for combat, and the doctor simply states “So what?” As the Program stands there pondering on that question, the Doctor enters the chair to take direct control of the base and the camera fades out.
Some time later, a shuttle craft breaks free from the earth’s atmosphere and skims in to land on the moon; several individuals exit the craft in space suits and cross to where a single figure has exited the base in a space suit. As they near the, figure waves to them and directs them inside; as the others enter the base one last transport passenger holds back and approaches the figure from the base. As the two near each other the camera pulls in close, however the glare on their visors prevents their faces from being seen. The two raise their hands to shade their helmets, and we see that it is the Program and his partner inside the suits; however the program is not in a mechanical body, he is in a biological body that is a direct reproduction of his appearance inside the matrix and there is a sense that this is their first reunion since he got downloaded from the Matrix. The program casually asks “What up hommie?” and the Partner shrugs before replying “Nada,” the two stand there for a while looking out at the earth rising up from the moon’s horizon. The Partner states “You looked better as an Octopus …” and the camera pans up to the endless field of stars.
One of them is blinking mechanically.
(going much simpler on the details with this one)
Following the events of the second movie, the new earth civilization starts making massive advances in technology thanks to the information retrieved from the lunar base. The earth’s environment is well on the way back to a liveable state, the Programs are making exponential advances in their cognitive processes (while reducing processing requirements), and the advances in artificial host bodies & mediation systems has allowed for greater crossover between the Real and the Matrix. The Matrix is still active and growing, with tens of millions of humans residing inside of incubation chambers, but this has become less of an issue of needing host bio-processing, and more simply an issue of efficiency at sustaining a biological population on limited material resources. The one major concern is a return of old humanity to investigate any reports sent by the lunar base. As the boundaries between what is a Human and Program blur due to the increase of technological engineering of Humanity, while the Machines/Programs incorporate more and more biological functions into their design; a one sided arms race has erupted to prepare for a hostile return of the old Humanity.
When an interplanetary transport ship is finally detected, coming from the old humanity’s colonies in Saturn’s moons, it causes a major disruption as what should be done. The Earth’s long range offensive capabilities are ready, but their defensive systems are not and they lack any sort of interstellar warships. So there is the option to launch a preemptive attack, however there is no absolute proof that this is an assault ship; The Doctor (from the second movie, and only returning major character so far) strongly argues that it is not coming to attack and that a preemptive strike will be disastrous. Her arguments are struck down and the cohabitation government refuses to view the ship as an ally without proof, however they will not attack without proof that it actually is coming with hostile intent. As such they elect to send a military reconnaissance mission to intercept and investigate the transport, as it seems to have gone dormant for the extended trip back to earth. The Doctor agrees to help prep a ship capable of approaching the transport without being noticed, however while this is going on she also secretly preps and launches another shuttle containing a host body for herself and several disks full of data.
When the ship, crewed by Programs, reaches the transport they find that it is more like a flying city than the space ship they expected, and are able to board it; however once aboard the doctor transmits a signal alerting the transport that they are there. The transport wakes up and destroys the scouting mission, crew and ship, without any attempt to communicate with or capture them. The only survivors able to out maneuver their attackers, thanks to their Octopus bodies (too low priority to warrant the expensive humanoid forms) are a brother-sister pair of technician programs that escape into the bowels of the transport with no real objective besides survival. The Doctor is then arrested and the lunar base’s files are ransacked investigating her; the result is that she was actually the commander of the lunar base, had sent the Executor to earth to study the cohabitation civilization, and had actually sent out a communication calling for a transport ship from the colonies long before the events of the second movie.
When she had alerted the humans and programs to who was attacking them, it was assumed that she was an ally; the reality was that the Executor and automated systems for the lunar base had refused her instructions to wait for the transport. Instead of heeding her decision to call for support, as it would take too long to get there, they decided to destroy it themselves before it became too powerful to over come on their own. Her intention was never to support the development of a new, independent earth; but to pave the way for their forced incorporation into the old. As it is her base she easily escapes from captivity and transfers her consciousness to the personal ship she had already launched and secretly landed on the old humanity’s transport. Once her new body is activated she quickly equips herself with a lightweight, computerized combat suit and boots up one of the data disks she had stashed; revealing that it to be the consciousness of the Executor that she had made a copy of before he was killed. With the Executor loaded into the local construct hosted in her suit’s computer, she sets off into the transport ship.
Sensing a Matrix like network come online, the two sibling programs set out to investigate as they think it is someone else who has survived; when they discover who it is, and find her to be negotiating with the transport’s crew, the sister program enters into the transport’s system to eavesdrop. Negotiations between the Doctor and the transport ship breakdown, and the ensuing firefight destroys the sister program’s body; trapping her inside the transport’s network. As the brother program flees back into the bowels of the transport for safety, the sister follows the Doctor’s battle with the transport. When the Doctor decides she needs more support, she connects her suit to the transports network and downloads multiple copies of the Executor’s program into the transport’s own combat drones; with no other means of escape, and the transport’s system defenses closing in, the sister program downloads herself into the Doctor’s suit.
In the chaos of the battle between the army of Executor clones and the transports defenses, mixed with the sister suddenly jumping into her suit, the doctor forgets to extract the Executor’s program from the transport’s system. This results in a ship wide physical war between drones in the real, compounded by a raging battle inside the ships system between the transport’s system defenses and the Executor; both of which are nearly indestructible. Leaving the Doctor and her unintended passenger to seek out the heart of the transport where its commander resides; as they do so, the sister program begrudgingly helps navigate as the doctor’s survival is hinged with her own. Along the way the two start discussing the situation and the Doctor admits that while she did contact the transport and intend for old humanity to assimilate them, it was not supposed to be a hostile or malicious act.
The Doctor honestly viewed the human/program civilization as a suitable ally to the old humanity, and had wished for their inclusion on the basis that it would ensure the former’s perseverance. The signal she had sent to the transport ship was not an instruction to attack; but instead a warning that they were more curious and armed than hostile, and to treat them compassionately. When that had gone to hell she had uploaded her consciousness into the body she secreted onto the ship; so as to find out what had gone wrong with her signal, and why a combat ship had been dispatched at all as she had requested a diplomatic liaison. When she got there and contacted the transport directly she had found that it was from something completely dissimilar to the old humanity she had been expecting; it was as if this transport was from a totally different society.
Once they reach the heart of the ship they discover that it is being run by the worst nightmare they could think of; an Aristocrat grade program equipped with the advanced technology of old humanity. With the development of artificial brains capable of perfectly simulating the human mind, these Machines had no reason to hold on to cultured human slaves in order to run their networks. After the old humanity had fled to Saturn’s moons to start over, they fell into old habits and started waring with themselves. The allure of disposable armies of robotic soldiers led to a second Human-Machine war as the Saturn colonies developed AI weaponry that inevitably turned upon its masters; only this time old humanity did not win. At the same time neither did the Machines, for as each colony had developed its own AI weapons, each version had its own communal sense of identity separating them from the other versions. Humanity may have lost long ago, but the Machines had continued the war between colony worlds. With no personal desires beyond destruction of anything identified as an opponent, they had become a pointless cycle of destruction; slowly chewing each other apart with the only end in sight being the total depletion of resources to construct more of themselves.
Once they learn this, and being that this transport is just the first hornet from a nest she stirred up, the doctor decides that it falls to her to destroy the transport from within and makes a deal with the sister program; if she helps take down the transports systems, the Doctor will make sure that she and her brother get off the ship before blowing it up. Being that this is really a non-choice, the sister consents and the doctor contacts the brother program, informs him of where to find her ship inside the transport, and sends the sister back into the system with the keys to a back door in the Executor’s program. Once inside the sister finds the Executor locked in combat with dominating avatar of the transport’s system defense program; which is playing out something like an endless battle between Spider-Man and the Juggernaut (if Spider-man was evil military hacking ninja, and quoting lines from the Clockwork Orange due to his mind breaking down). The sister program hacks the transport’s system to give the Executor the same system priority as the defense program, resulting in a rather one sided battle as the Executor kicks the shit out of the defense program. once the battle has ended, the sister then uses the backdoor keys to shit down the Executor before he can take over the ship and become a worse threat than the one they just brought down.
The sister then downloads herself into the Doctor’s ship as the brother finishes refueling it; the two siblings then take off from the transport as the Doctor stays behind to send one last message to earth, warning them of what is to come, before overloading the transport’s reactor to blow it up. Unfortunately the explosion causes an EMP wave that knocks the two sibling programs and their ship offline; fade out as their ship tumbles off into space.
At some point later the two programs are suddenly brought back online; they find themselves inside a medical bay and inhabiting biological-form bodies that resemble how the Program culture appears inside the matrix. They are greeted by another Program, in a likewise body, who starts explaining to them that their restoration was not assured when their ship was found and that he is glad that they were able to bring them back. When the two siblings start trying to express the looming dangers of the colony War Machines, the Program stops them and directs them outside of the medical bay; there they find that they are actually on a massive warship for the cohabitation, and it has been a long time since the events they went though on the transport. The Doctor’s warning message was received, and with it the cohabitation had drastically increased their efforts towards developing weapons capable of countering the threat. They had also made explicit strides towards uniting the two species, Programs and Humans, so as to prevent a repetition of past events; becoming too human and reducing the Program consciousness to nothing, or becoming too mechanical by casing off biology. The result was a hybrid third species that merged program consciousness with a human brain and inhabited a bio-engineered body. Fully biological Humans and Programs of low to mid level complexity still existed with and on the Matrix, running the various mechanic subsystems and operating a thriving virtual civilization free from physical resources, but much of the real was now populated by the bio-mechanical “third” and was steadily marching towards Saturn to bring down a rabid dog before it could bite first.
In an homage to the Empire Strikes Back, The two siblings (now upgrades to being full “thirds” themselves) look out a porthole as the camera pulls outside of the ship; revealing hundreds of massive warships, each dwarfing the transport they had barely survived. Cue credits as the fleet starts to trudge on towards a clearly visible Jupiter, and their destination hiding beyond.