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By the year 2060, human civilization on Earth has been ravaged by war, famine, polution and poverty.
In a final attempt to restart humanity, the "United Nations" send a colony ship to Alpha Centauri called the "Unity".
Ten thousand crew and colonists, under the leadership of Captain Garland and bearing nothing to signify their country of origin, are placed in cryogenic sleep. They depart on a decades long journey to colonize the planet "Chiron" in the Alpha Centauri system.
Forty years pass without incident to ship or crew. With the Unity only days away from planetfall, a core malfunction awakens the crew prematurely. As they attempt repairs, an unknown assailant kills the ship's captain. Panic and confusion follow in its wake. Seven leaders are able to restore order but it comes at the cost of the original mission. The colonists reorganize themselves into seven groups, each following one of the leaders. Aligned now not by nationality but by ideology, each faction takes control of a colony pod. The Unity, its operations neglected, breaks apart in high orbit around Chiron, now named "Planet." Colony pods, resources and supplies are scattered on the surface and humanity begins constructing civilization anew, each faction cut off from each other.
Chiron has a toxic atmosphere for humans, who require vacuum suites to survive outdoors, but the highly noxious environment turns out to work very well for earth plants, so terran crops are able to be farmed in Chrion's soil. Each faction continues to build and develop on its own, applying their own values and in due time resume conflict and warfare as their ideologies or goals conflict.
One of the faction called the "Gaians" discovers that this is not an ordinary planet, but some strange force seems to guide and design the flora (xenofungus) and fauna (various form of mindworms).
After several years on "Planet", 2 alien ships arrive in Planets atmosphere, fighting each other, resulting in both of them also crashlanding on Planets surface. Both of these alien factions seem to be of the same race (Progenitors) but with conflicting and competing ideologies. At first they are unable to communicate with humans. The Progenitors have evolved complex biological systems that can sense fields imperceptible to humans, including at least electrical and magnetic fields. The collective term for this sensitivity is resonance, and permeates all Progenitor communication, art, and culture but also combat. Planet contains various ruins and artifacts of Progenitor origin, indicating that they have a past with Planet.
Human survival and expansion is tough due to fighting among the human factions, brutal conflicts with Progenitor factions involving genocide and other atrocities on both sides, but one of the biggest dangers for all are the native fauna and flora of Planet: the Xenofungus and various form of mindworms that use "psi combat" which makes high-tech weaponry basically obsolete and victory is determined by sheer willpower and morale. Several technological breakthroughs allow humans to increase their odds in psi combat, but also lead to discovery of the nature and origin of Planet.
Planet is not a spontaneously generated planet, but an living entity consisting of a vast neural network serving as Chiron's "brain" that controls the mindworm as a defense mechanism on anything that threatons its existence or natural resources. Any ecological damage on Planet, gets retaliated with massive mindworm attacks against the perpetrator in the form of psi attacks.
Through more research of various Progenitor artifacts and study of Planet, eventually 1 of the human factions (presumably the Gaians) manage to make telepathical contact with Chiron. Chirons communication is simple at first, and tries to warn humanity, of what is not immediately clear. As the years continue, and the xenofungus continues to grow faster and faster, the interactions with Chiron become more clear, and there are direct warnings agains humanities ecological damage on Planet and that there will be consequences. Indeed, factions that contribute more ecological damage through mining and polution get far more numerous and more vicious mindworm attacks, and find their buildings and cities themselves overrun and damaged by rapidly growing xenofungus. Some loose entire cities.
As the xenofungus network grows, and humanity creates certain devices to better communicate with Planet, they learn of Planets past, and the role of the Progenitors in its creation.
The humans find out that Planet is stuck in a vicious cycle where every x millenia the neural network/xenofungus grows exponentially consuming all life on planet, and then, starved of resources and nutrients, most of the xenofungus dies off and the Planetmind is reverted back into a slumbering state.
Also discovered is that Planet is one of several creations of the Progenitor race in a long and distant past, called a "Manifold". Manifolds were galactic level experiments by the Progenitors millenia ago in an attempt to achieve a form of godhood, but all the other experiments ended with the Manifold taking over and consuming entire solar systems occupied by Progenitors, and almost completely destroying their civilization, and plunging them into a kind of dark age in which most of their knowledge and technology was lost.
The 2 Progenitor factions fight over the use of Planet; one faction, calling themselves the Manifold Usurpers wants gain complete control (by eliminating the other Progenitor faction and all of humanity) in order to repeat and complete the experiment, while the other, called Manifold Caretakers wants to leave Planet the way it is, but is also determined to destroy the other progenitor faction and humanity with it to ensure this goal.
Eventually a human faction (most likely the Gaians) discover a way to convince Planet to delay the growth cycle, and to allow humanity to "Transcend" together with Planetmind, starting a posthuman era, in a form very closely related to the idea of the technological singularity. After this project is built the human inhabitants of Chiron who chose to do so leave their material bodies to merge with the emerged planet intelligence, and continue to manage Planet, turning its atmosphere into oxygen, making it breathable for humans who decide to live out natural lives. Despite several attempts, no contact with Earth was able to be established, and it is assumed that this is all that is left of humanity.