Here's what I think...
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The end of the war had come. The green Darwinians had been saved, thanks to Dr. Sepulveda and the Unidentified. Without the Unidentified's help, the global reset button would have been pushed for sure. When he and the Darwinian army arrived to begin work on cleaning out the Temple, the few reds who had seen what the greens were capable of, stole several Armors and drove their way from the Biosphere, all the way to the God Dish. Before the Spam could remotely stop them with their flying corrupters, the reds opened the link and flew their armors up into the Soul Repository.
Upon arriving, they began to see the truth about their world, and their corruption of the Virus. They saw many beautiful things to behold, one which no Darwinian could ever remember, even if reprocessed after death. This is what ultimately began to make the reds shake their bindings of the Virus on them. However, they noticed that they, and the armor they were sitting in, was beginning to decay as bits of code was flying off and separating from them. Realizing that in order to avoid death, they had to get out... this means falling out of the sky, sure, but they had an idea...
In order to slow their fall, they would have to follow the slow trail of souls down to the receivers. It took them a half hour to get down, as the surface from Darwinia to the Soul Repository was estimated to have been several hundred miles, in Darwinian length.) Upon breaking the surface of the Receiver area, the souls began to scatter... and so did their slowing cushion. The few armors riding the waves of souls, acted like meteors and crashed into several of the receivers. The Darwinians around fled the scene, noticing the area was beginning to glitch like crazy.
The reds managed to survive mostly, albeit a few had broken-off body parts which they attempted to put back on. They took the souls of those who had died and placed them directly onto a receiver head which was now bent over to the point where a Darwinian could touch it. Watching with amazement, the souls latched onto the rail and zipped away to be processed. They began to search around secretly for another armor, in which there was one near the Pattern Buffer trunkport, hijacked it, and drove through the port.
Under the guise of a green Darwinian transport, they were allowed to look around to see if anything changed from the damage they caused. It only was until a few minutes later that all Darwinians present began to see the pattern glitch out. Souls moved at random speeds, bumping into one another as they slid along the rail lines to be processed. Some of them caused the pattern to fizzle and make odd minor color changes to the image, even make a few odd Darwinians with antennas, and different shades of green.
The surviving reds quickly traveled through back to the Biosphere to look at what was going on. Darwinians were suddenly beginning to spawn like crazy, and many of them had the ability to change their colors, some of them having antennas. Those who decided "red" was a cool color were immediately fired upon from the prestigious greens, fearing they might be the viral Darwinians.
These new Darwinians, thinking they would be ultimately the starting of a new race, immediately began to make their way through the Yard's trunkport. Out of the Temple port flew what they recognized as Sepulveda's and Unidentified's presences, and watched as they went to the Yard. The reds followed behind, and began to pick up messages that these newly found Darwinians were sending to Sepulveda's computer. Such messages stated they wished to create a new colored faction and become the founders, and asked to be provided with materials to build new trunkports, receivers, spawn links, spawn points, etc.
Realizing this was possibly the start of a new era, Sepulveda authorized and reconfigured the yard's construction mechanism to build whole entire buildings on enormous-sized Armors, capable of carrying up to 2000 Darwinians. They took more time, power, and resources to build--rumors are that the Mining facilities were being ordered to bigger continents to do some more mining from fresh depots. These new armors helped set up new trunkports all around the world of their current existing states. They began to reconfigure everything they built... including the spawn points.
The old systems were disassembled and made to work and cooperate with the new ones, and the Spawn Master was rebuilt from scratch as well. Instead of sending a soul to a spawn point per two seconds, it now sends twenty souls over five seconds, and rests for ten. The bottleneck launchers at the end of the new spawn point systems prevent chronic congestion on the exit hall so Darwinians wouldn't have to wait for the crowd to clear out.
Many of these new colored-based Darwinians began to call themselves Multiwinians and began to inhabit much larger islands for their home systems. Dr. Sepulveda was astounded at how many more places began to recreate the original systems, only much closer to their new "homeland" spawn systems, even making their own spawn masters, as some "tribes" as they began to call themselves had difficulty in programming their trunkports to send souls from the original Pattern Buffer. These new spawn points also made Incubators obsolete, as Engineers now had the ability to take souls and deposit them directly into the coding sphere of the Spawn points, thanks to Sepulveda's minor recoding sources of Darwinian/Multiwinian souls.
Even the small red tribe that escaped with the armor managed to colonize and reproduce at a rapid rate. To show they were not in league with the virus, they pointed out to several other co-existing tribes, namely the blues and yellows, that a small island the reds were trying to contain, the virus had evolved into a black color. They even demonstrated by launching some of their own eggs at the black virii. The new version of the Eggs Dr. Sepulveda had made for all sides were allowed to hatch all versions of team-friendly viruses. He had attempted an experiment to place in Soul Destroyers, but it had failed, and that included taking out the soul destructing code to allow souls to remain behind, and took the code out from the eggs entirely. However, a few unwitting green Darwinians took the soul of an old soul destroyer and uplinked it with the rest of the eggs, thinking it would help defend them if ever need be. This caused the red's eggs to hatch a black soul destroyer which annihilated the red virii, and they were forced to evacuate and shut down the trunk port, disassembling it entirely for the safety of the rest of the tribes.
But before that happened, the new Virus managed to steal a few multiwinians, killed them, and reformed their body code, creating the Evilwinians. A long fight between the Red multiwinians and the evilwinians took place. The multiwinians quickly learned of the new viral warfare the Virus had created, such as erupting Ants nests, twisted trees called Dark Forests which acted like Soul destroyers to any multiwinians who got close them, and even stole/infected many crates which were used by aircrafts to be deposited to tribes in need. The new crates acted just like the spam cubes once opened, only with the added option to turn multiwinians into evilwinians. These evilwinians were in alliance with the viruses, so even if the multiwinians did manage to obtain how to use the viral weaponry, it would only fuel the fire against them.
During a severely lopsided battle with the Reds loosing, and on the brink of losing that island post, a large alien spacecraft came down and began to suck up evilwinians left and right, saving the reds. After a small amount of time, they then began to beam down white, glowing, antenna equipped multiwinians that glowed brightly, and fought back the Virus with a new weapon called Subversion, which replaced their original lasers with small, slow, powerful bolts that turned enemy multiwinians into their version of multiwinians. They introduced themselves as the Futurewinians, and offered to help fight back the virus.
While this new weaponry was being duplicated into exact replicas by all the tribes working together, the Futurewinians warned that grenade technology was now obsolete thanks to this new weapon they've made as they think it causes too many casualties to those who use it the most. Residing with the reds, the Futurewinians combined their new technology with the grenade/rocket toting multiwinians, and began to finally make a stand against the Virus on their islands. Things seemed to finally be turning the other cheek for the reds.
But it wasn't over. There was still the epic "Last Stand" battle to go. The virus, desperately looking for a way to get back into controlling the reds, performed various stunts and snuck into an enormous cache of crates, stealing half of them, and leaving the rest of the crates with a new weapon of theirs--the Randomiser, and the Plague Outbreak. The virus, overtime, was beginning to care less about attempting to steal the souls, and finally decided to just destroy every part of the new Darwinia if they could. These weapons pushed the futurewinians and redwinians back to the Red's main homeland, where a final battle began to surmount. They fought for several weeks before the Virus began to slowly push an edge over them. Down to the last ten spawn points and about to become overwhelmed, a large series of airstrikes bombarded the Virus, and fifty green armors rolled in, deploying many green Multiwinians, who began to work with the futures and reds, deploying a whole arsenal of nuclear strikes and causing enormous meteor showers, two weapons they have just made. Dr. Sepulveda had arrived, leading the greens to help out the reds. Granted the rest of the spawn points for the remainder of the battle, the reds safe-housed the rest of the power-ups and kept them safe while the greens, with their Subversion/Grenade combo proved to be the ultimate weapon in driving the virus out of the red's homeland, and poured into the Virus's trunk port, destroying it and causing a massive influx in the teleport shield, it detonated the entire island the Virus was on and caused it to sink under the ocean.
Hearing of the final defeat and riddance of the Virus, all tribes celebrated together with the influence of Sepulveda. Having permanently stashed the code away for good, the Virus was now no more. The futurewinians decided not to stay, and left with their many spacecrafts, leaving the red islands for the time being. With the help of Sepulveda, they constructed three councils with trunk ports leading to each other--War, Peace, and Neutral councils. All the 9 different colored tribes were given these buildings to discuss keeping peace and to help maintain evolutionary growth, as they had been evolving rapidly over the passing years.
Several groups began to form amongst the Greens and Reds, however... This is when Sepulveda eventually began to notice some slight unrest between the greens and reds. They began to crave expanding their islands, and began to think the two were intermingling too much to the point where they were close enough to cause huge amounts of chaos, and wipe each other out must history repeat itself. The radical groups wanted to continue war against each other.
The greens wanted to continue, stating that if it hadn't been for the reds, there would be no virii, no war, and no possibilities of loss of life. The reds argued that the greens were originally responsible because they downloaded the spam from Sepulveda's computer. Sepulveda, tired of seeing the two getting so heated up, sent down Futurewinians to help keep the two separated, and for the time being, forced both sides to stay on their own islands.
However, this only seemed to aggrovate a few of the green zealots of war. They disguised themselves as red multiwinians and secretly took over a spawn point, only revealing themselves when they had enough to start a large fight against the reds. Horrified, Dr. Sepulveda initialized "Code 805" to the Futurewinians. Every multiwinian knew that that code meant certain death for them. The futurewinians immediately began to fire upon and convert any nearby 'winian, regardless of color, in order to cover up the fighting so as to not provide influence to the other tribes to seize the opportunity to expand by force. While the Futurewinians did win, word spread like fire, and many 'winians flocked to the site to see what was going on, but the futures forced them back. The reds lead a massive attack against the Futurewinians however, knowing what the Futurewinians were fully capable of doing and what they couldn't do, and used whatever edge they had, including rocket and grenade barrages. They wiped the futurewinians off the surface of the red's home land and restored order to their namesake.
Furious, Sepulveda extracted a backup of the virus code they had just stashed and began to unleash it to teach the multiwinians a hard-to-learn lesson. At the same time, Sepulveda set up another new Darwinia, renaming the old Darwinia Multiwinia, and evacuated all original Darwinians, and shut down the link between the two worlds. At least the Darwinians could now live in peace and harmony, away from the hell-infected Multiwinia. At that point, wanting nothing more to do with the Multiwinians, he opened ports for regular human beings to take control of static points, influence random sets of Multiwinians to their will, and cause warfare by any means necessary. However, the Multiwinians were prepared this time, and several hours after Sepulveda unleashed it, it was immediately destroyed for good, except for the remaining crates that contain the infections. Sepulveda hasn't touched his old console for several years now... He only keeps to his new Darwinians with the help of Unidentified to this day...
He didn't want to pull the plug on the power though, as he cared for the Multiwinians too much to let them just get shut down, and so hopes that humanity will influence peace during the time of the Unending war.
When and how it will happen, we may not know in this lifetime...
That's what I think anyway. Post your thoughts here.