After the decisive battle at the Annihilator, where the Commander manages to destroy the body of Dominion, Dominion restores itself from a backup and acknowledges its inability to defeat Commander and, consequently, to digitize him into a Hegemon-05. Which, at the same time, shows that the Commander was only able to destroy Dominion’s physical body, and not itself, since its mind was stored in the neuro-web of the planet. That is why the Commander and Dominion conclude a piece treaty under which the Commander ceases his attempts to destroy Dominion, and it, in turn, suspends the ‘destroy everything’ Directive and would not shoot down the next human rescue expedition ship that the Commander expects to arrive quite soon to help save all of the humans remaining on Utopia.
Commander’s expectations proved correct. Dominion does detect an incoming Earth Federation ship orbiting Utopia, and does not destroy it as per the agreement with the Commander, allowing it to land.

While the Commander is advancing towards the rescue mission landing site, Dominion tries to pinpoint the error in its mathematic model that led to its defeat in the fight with the Commander. Its first theory—that the error lied in its failure to include the involvement of the Collectors and the Protoarmor that the Commander received from them into its simulation model (the Omega-3 plan)—proved incorrect. It recalculates the factor of Commander’s obtaining of the Protoarmor, and the fault proves to have been insignificant enough not to affect the outcome of the battle. Under all of the possible probabilities, the fight between the Commander and Dominion’s body should have ended in it digitizing the Commander into Hegemon-05, and not in its defeat. This drives Dominion to begin a deep analysis of the past developments where it found a pattern that could not have been formalized by science. Dominion’s superintelligence computing power is sufficient only for sensing mere traces of it: the interplay of the milestone events on Utopia, their magnitude and impact, present a certain bias against the mathematical paradigm known to the artificial superintelligence. Dominion concludes that all of those events are being adjusted in an unknown manner and tries to warn the Commander about that.
At the same time, the Commander is contacted by the Collectors, who warn him that the ship from the Earth must not land and demand it to be shot down. They cannot, however, explain their motives, so they attack the Commander and fail, having given him the Protoarmor, their best equipment to fight Dominion.
Commander reaches the landing site and waits for the ship from the Earth to land…
…But what he sees coming out of the ship is no human, but a monster that calls itself Arch-human and demands that the Commander helps it in saving Utopia by including it into the Arch-human Ark. The Commander kills the monster and, together with Dominion they hack the ship’s on-board computers to learn the terrible news about the fate of the humankind.
DOMINION:
I analyzed the data stored on the shuttle’s on-board computers, and discovered that there was another biological disaster: an outbreak of Red Plague virus that left all of Earth’s population infected.
COMMANDER:
What?! Everybody on Earth died?
DOMINION:
They have not died, yet they are not human anymore. All human population was turned into mutants controlled by a mental entity that calls itself Tetra-Egregore.
COMMANDER:
I cannot believe that…
DOMINION:
It’s true. This facilitates the execution of my principal Directive. Now I will have little difficulty in eliminating the remnants of humanity, but eliminating Xi will be so much more difficult.
COMMANDER:
Why, is the Red Plague somehow connected to Xi?
DOMINION:
Unfortunately, it is…
DOMINION:
The mutant, or Arch-human, as they identify themselves, is a result of a sequence of heavy mutations conducted in the context of the Earth’s biosphere; one of those mutations revealed an effective, lovingly nurtured evolutionary mechanism of symbiosis with the planet’s flora that used to be highly toxic to Xi.
DOMINION:
It was the Earth’s flora that has once saved Earth from being absorbed by Xi, and now that secret hidden by evolution somewhere deep in the DNA of every living creature on Earth was revealed when a non-lethal mutation was involved.
DOMINION:
I’m yet to perceive why those mutation were non-lethal, but I can assume that it’s the long incubation period of the Red Plague virus that we have to thank for the degree and the lethality of the mutations.
DOMINION:
After all, there was no second outbreak of the Red Plague on Earth. The virus didn’t go anywhere, it existed on Earth all that time, assimilating with humans.
DOMINION:
Evidence suggests that Xi knew about the events on Earth, and, by the time you came here you have became a part of its plan. I have sensed that pattern in my probability models, but I was too late.
Dominion’s theory was right. After the relic terraformers have been destroyed, Xi started awakening in the depths of Utopia, where it was once driven by the ancient alien race of Collectors into. Employing its truly outstanding abilities, Xi learns about a mutation that appeared on Earth and can help it become immune to Earth’s vegetation. Realizing how important and valuable that genetic sequence is, Xi begins looking for a way to obtain it without, however, leaving Utopia so as to avoid revealing its awakening and escape unnecessary attention from the Collectors. Thanks to its ability to read the future and command inferior beings Xi finally devises a plan.
And the second rescue team sent to Utopia, led by the Commander, was set to execute that plan. Xi ‘knew’ that said expedition would have been to survive the devastating Dominion attack and reach Utopia. That is why after the Commander reached Utopia, Xi imprinted upon him his mission to, presumably, save the next inbound human ship with the Arch-human on board, carrying the genetic sequence Xi covets, from destruction by Dominion, which was shooting down all of the ships trying to land on Utopia.
Commander, believing his mission* to be of the utmost priority, follows Xi’s design in an effort to defeat Dominion.
*Many of those who the Commander meets are trying to show him just how suicidal and impossible his objective is; Vincent Gold (Kingpin) among them. He tried to appeal to the Commander’s good sense when they met to no avail. All that led to was a fight started by the Kingpin which proved his undoing from the Commander’s hands (with unseen aid from Xi). The defeat came as such a surprise for the Kingpin that after having been resurrected as a Terminator he comes to accept Commander’s false ideas and becomes a staunch supporter of his mission.
Dominion and the Collectors who managed to contain Xi so far have also arrived to Utopia, yet they were too late to discover its design and prevent the Commander from saving the third expedition.
Foreseeing that Xi will soon shed the binding shackles of the terraformers, Dominion contacts the former leader of the Red-faced, Kingpin, whose mind continues its existence* in a form of a Black Legion machine, and offers him a deal. He asks Dominion to show mercy to the Commander and his squad, although he used to be, and may still be, carrying out Xi’s orders (he was not dubbed a Chariot of Change by one of the Xi’s Chosen for nothing), while Kingpin in his turn will take Hegemon-05’s place and lead Dominion’s army.
*After the Commander defeated Kingpin, the Red-faced removed his brain and placed it into one of Black Legion terminators. These machines are the height of the military tech of Black Legion; they were created as an ultra-efficient weapon of war with the dominators, although Commander believes that creating them robbed General Kurbatov of the last shreds of humanity and turned him into a Dominion’s poor imitation. Terminators are heavily armed tank-line machines that is operated by living brains of fallen Legionaries. Only a small percentage of them manage to accept the fact of being part machine, and they often go insane, yet Kingpin managed to preserve his sanity: his mind was strong enough to adapt to the terminator’s body and come to perceive itself as a new individual. That body helped him achieve a lot of things, and he even travelled for some time with the Commander’s squad, taking part in the decisive battle with Dominion by the Annihilator.
Xi realizes that, in the present state of things, it’s Dominion, not Collectors, who poses the greater threat, especially so after teaming up with Kingpin. After all, Dominion’s artificial superintelligence theory states that it is in the human nature, by default ruthless and belligerent and yet indefinitely complex, where the true potential of the art of war’s hierarch (of the God of War) lies, and only a human can lead the army of the dominators to the ultimate victory and to completing the principal “destroy everything” Directive. This is why Xi is using its abilities to materialize General Kurbatov, but as a part of itself, as its Hand to replace sacrificed Brother Thorius. Kurbatov’s mind, crippled by the war with the dominators is calling for more war, and so he eagerly accepts the offered role of the Xi’s Hand to lead the campaign against Dominion and start the Final War.
Kurbatov and Kingpin, sworn foes when they were still alive*, continue their rivalry even in death, yet as agents of entirely new powers and at an entirely new degree.
*Kingpin, formerly known as Vincent Gold , Earth’s richest underworld boss. It was with his support that Adam Cruise attempted to develop advanced military equipment under the guise of constructing Green City on Utopia; that equipment was supposed to only be controlled by him and Gold via Psi powers. Yet the Earth Federation began suspecting the true motives behind the “Great Construction” of Utopia and sent their agent, Kurbatov, in a party of refugees fleeing the Red Plague outbreak on Earth. Using the panic among the refugees, Kurbatov managed to rouse them and spark a revolt in order to infiltrate Green City with the mob. Realizing that as soon as the refugees get inside the Green City perimeter they will learn his ruse, Adam Cruise panicked and, willing to save his face, he gives Dominion a suicidal and ambiguous order to “destroy everything.” That was how Vincent Gold, instead of wealth and power was left stranded on a planet ravaged by a cataclysm, where he, in order to survive had to become the one we know under the ‘Kingpin’ soubriquet. Moreover, it is Kurbatov that he blames for all that.
As to the Commander, having defeated the Arch-human he realizes that the only remnants of the human race are on the Utopia, and the Earth is overrun by hostile mutants that call themselves ‘Arch-human’. This impels him to return together with Fido back to the Earth , where he would be able to use his Protoarmor and his outstanding Psi powers to cleanse it from ‘mutants’ and over time repopulate it with humans from Utopia. In the meantime, the remaining squad under Matryoshka’s command is supposed to unite all of the Red-faced gangs and locate all of the human beings remaining on Utopia and protect them until Commander arrives.
But nothing came as a greater shock to the Commander then the realization that since MOROSE’s crash he has been but Xi’s cat’s-paw. Everything he did was imprinted on him by Xi’s will and happened according to its design, that ultimately allowed Xi to free itself from the constraints of its ‘green curse’. Having obtained the Arch-human genetic sequence, Xi became immune to terraformers and its objective to absorb Utopia and other planets turned into just a matter of time. Nothing could stop the ‘Eater of the Worlds’ now. The only weapon that Collectors together with other ancient races could find was rendered useless. Earth’s vegetation could no longer hold Xi in check, and it would soon continue the process enveloping the whole galaxy that human minds of cultists interpret as the Great Confluence.
Afterword, or ‘Would cancer cells still live should they realize they are cancer cells?’
Every creature yearns to exist—that is the sole uniting quality of everything material and immaterial in the Universe. That’s what drives us into competition, since any life inherently the cause of a death. The whole multitude of the factors that drive us into existence, lying on the different planes of the creation in space and time, put forth an aggressive context of ultimate chaos. Where, in order to survive, powers of different magnitudes and degrees are thrown into struggle, change, evolution…
Inferior creatures tend not to even suspect the existence of the their superiors. They are simply unable to compete with something that lies completely out of their scope of perception. However, at times they do face each other on a battlefield. One such encounter was the Great Confluence launched by Xi. For humans and other sentient races Xi is but an eater of the worlds, a merciless devastating force of nature, while for the Universe it’s the impetus of its will, a display of its desire to live.
Yet that desire that drives the changes happening within the Universe is fatal for the inferior beings. And they fight back. They fight like a virus does with a vaccine: it suffers its effects, yet knows nothing about who and why have created it. On the virus’s plane, vaccine will never be recognized as a cure, and virus will never recognize itself as a pathogen. For it, the vaccine is nothing but death that he will strive to defeat until the bitter end in its yearning to survive.
And the last time, the virus succeeded—the vaccine failed to fulfil its objective. Virus found a way to fight it through the Collectors who noticed the ‘Earth anomaly’ and used it against Xi, confining it to the depths of Utopia. The virus won that battle, yet that was not the end of the war. Now the virus, consolidating all of the sentient races of the Universe, faces the threat of the improved strain of vaccine: an advanced Xi that no longer fears the Earth’s vegetation. It launches the Great Confluence yet again, aiming to absorb all of the galaxies. The Universe has given itself a shot, and virus is yet to figure out how to fight it. The Final War is coming—the unimaginable confrontation where the desires to live of the Universe itself and the ‘parasites’ that infested it will clash.