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Basic Premise
The game(s) is set in a "post-modern, post-apocalyptic world where every human is a mutant of some sorts" world. It revolves around the question "what does it mean to be a human" to the extreme, with each mutant species convinced that they are the logical next step for the human species, while viewing the rest as nothing more than failed evolutionary variants.
This is more "what does it mean to be racist", as there's no question that everybody is a divergent human, not something different and subhuman: do you think other mutants are "bad" or "inferior", or people like you?
A war about resources and land is also quite orthogonal to racial concerns: all assorted mutants from Here vs the same kinds of mutants from Over There are much more plausible factions than vanishingly small mutant races.
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The game's aesthetics resemble an apocalyptic parody of modern day life, with a slight touch of advanced technologies like hydroplasma cells, rail guns, powered exoskeleton suits and advanced all-terrain personal hovercrafts.
Not the simple and rugged technology that can work after a complete industrial collapse.
"Advanced technology" would be keeping anything requiring fossil fuels or electric power operating.
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And it is in this world that the player creates their own story - of their journeys in the desolate and deadly Wildlands where every next step could very well be their last.
There must be some damn good places to go if the Wildlands are so dangerous.
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Cause of Apocalypse
The world woke up one day in the near future (2013 to be certain) and realized that all the world's leaders have boarded into 7 massive Eden ships and fled into space,
There's no way a conspiracy of this size can remain secret.
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leaving the world behind to total anarchy.
Either an excessive number of people (in the order of many millions) flee, which is even more preposterous, or perfectly qualified people take over governments and prevent anarchy.
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For the first week there were riots and skirmishes all over the globe as people scrambled to fill in the leadership void;
No, only in specific trouble spots. Given the epidemic that follows, this sort of turmoil seems unnecessary to explain a post-apocalyptic situation.
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but just when things were starting to sort itself out a deadly epidemic broke out all over the globe, wiping out tens of millions every day.
Too sudden for any reasonable means of natural diffusion; tens of millions of victims every day can only be the apex of a months-long epidemic.
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In mere months the entire world's population had been reduced to mere millions, who no longer had any food left as the virus affected all living beings.
Not bloody likely. Viruses work only on a narrow range of similar species; killing humans and apes with the same disease would already stretch disbelief.
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The general consensus amongst the survivors of the First Deadly Epidemic was that those who left in the Eden ships foresaw the apocalypse event, and rather than fighting it they fled instead. The exodus would come to be known as the Great Desertion in history, and turned into the source of universal hatred and blame amongst the survivors of the epidemic.
I'd rather think they caused the epidemic, unless you postulate precognition powers.
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South East Asia Survives
Miraculously, survivors of the epidemic found out that South East Asia were largely untouched by the epidemic,
Beyond impossible, since southeast Asia has international airports like everybody else and high population densities in many places. There might be a contrived explanation at the end of the game, but the damage is already done.
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as well as isolated islands in the Pacific and Atlantic oceans.
More reasonable, but be consistent.
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Knowing that their survival now hinged on the small little third world continent, survivors from all over the world packed up their gears and made the long journey to the last sanctuary on the planet.
Without transportation? And why risk life to crowd an already crowded place instead of spreading out at home?
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For a while the South East Asians welcomed these people with open arms: a testimony of humanity and compassion long thought forgotten in the cynical and apathetic first world.
However, as more congregated in the continent, resources began to dwindle and soon a deadly tension between the natives and the foreigners threaten to spiral chaotically out of control.
What exactly about shooting harmless refugees from land and sinking harmless refugees on boats can "spiral out of control"?
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The Outsider Wars
Nobody remembered how it happened, but the uncomfortable tolerance between the natives and the foreigners finally broke in the year 2014, one year after they voluntarily offered their homes and food to these immigrants.
Quarrels quickly escalated into skirmishes, and subsequently into total war. Thousands laid dead every day from raids and ambushes, and rival villages and towns sent war bands against each other for all sorts of reasons, of which many of them were trivial in retrospect.
This sort of conflict can develop anywhere, not only in special southeast Asia, as old civilization resources dwindle.
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Though the exact cause for the Outsider Wars would probably be lost in the annals of oral history, one thing remained for certain: the war became the herald of the dark age and the dawn of mutantkind when one of the skirmishes accidentally destroyed an experimental research facility, which released gallons of mutagens into the atmosphere.
An unlikely and unjustified addition of insult to injury.
A global mutagenic contamination would require a huge amount of mutagens, not "gallons". I suggest instead a plain old thermonuclear war: a classic cause of genetic mutation, and a grand goodbye to the technology that made it possible and won't come back.
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The Dark Age
The airborne mutagen were not detected until years later
9 months lather, obviously.
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when its effects began to manifest. Babies were born with severe defects and adults began suffering from strange and incurable diseases. More people died of cancer than bullets, and soon scientists came to the harrowing conclusion that South East Asia was no longer safe anymore.
Protective gear
No, at that point everyone has already been exposed. In the best case scenario, healthy people do not have the means to keep themselves protected all the time forever.
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were quickly issued to all those who could afford it, and for the unfortunate they either stole or murdered for it. Travel became tedious and dangerous, resulting in communities being isolated from one another as time went by.
Wasn't everybody at war with their neighbours?
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Not every community were fortunate enough to receive these protective measures however, and were forced to weather the mutations. Tens of thousands of deaths through cancer and diseases soon paved the way to a new generation of mutant variants.
The Mutant Dawn
While many humans were killed by malicious mutations, small numbers of them benefited from it instead, providing them with new means to survive the desolate lands.
We are talking about VERY few survivors, in a completely collapsed society.
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Soon, their fortune spilled over to their descendants, and from their bloodline came a new generation of humans who bore little to no resemblance to pre-desertion humans, but retained similar culture, mannerism, tradition and lifestyles.
No, how can small bands of hunters/gatherers or possibly farmers resemble the former civilization? At best they still have books.
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Communities blessed with protective gear believe themselves as the last remaining "pure" humans, and zealously enforce this fact by exiling/executing any community members who display but the slightest sign of mutation. This xenophobic zeal soon redirected its attention outwards, and a genocidal scheme soon brought these communities together in unity. They formed the Confederacy of Pure Humans, locked and loaded their firearms, and launched the Great Purge.
I'd think survival and reproduction would have a greater priority than genocide and racism.
Protective gear is, I repeat, very unlikely. Can't you limit yourself to different mutants?
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The mutants were caught by surprise as armies of biohazard suited clad militias tore into their peaceful villages and slaughtered every men, women and children. At first the mutants fled from the "Pure Men", but soon they began to fight back. The mutants rallied under the inspirations of a visionary mutant by the name of Criss,
You are implying an unrealistic, excessive amount of technology, population, economic surplus, hate, and communication capabilities.
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who then formed the Crissen Order whose membership was open to any mutant who were ready to shed blood for the better of mutantkind.
The war between the Confederacy and the Order ground down to a stalemate in the fields of Blacksand before a massive pre-desertion metropolis ruins, dying the earth red with the blood of the fallen. It was there upon the stained grounds that both sides began questioning of the reason for warfare. For the first time in centuries of bloodshed, they finally pondered about peace.
The Combine
The Confederacy and the Crissen Order finally merged after a long truce, uniting into a new entity called the Combine that promised a fair future where mutants and pure humans could live alongside each other in peace.
Because many were unprepared to discard their prejudices and vendettas for fallen comrades and family, the early days of the Combine were stricken by many difficulties; many of which led to brawls, murders and discriminations. Legislation of a constitution that advocated the superiority of the Pure Men (who happened to be the majority race in the Combine) led to even more dissatisfactions, and soon a scheme was hatched to wrestle the society under control.
So the "Pure Men" won; but they can only be a small minority, and they should be mutated by this point.
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From the vaults of pre-desertion technologies the high council of the Combine approved the release of the same virus that wiped out all civilizations after the desertion.
It's still out there, preserved in huge amounts in nature and culling the few people who aren't born with immunity, without further epidemic diffusion.
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The virus was deployed in the guise of a research facility accident, which many found to be questionable given the high council's lackluster efforts at containing the spread. Citizens of the Combine were then forced to wear the same biohazard suits that were once associated with the very identities of the Pure Men in order to survive the Second Deadly Epidemic.
As if there are biohazard suits for everyone, I mean for anyone.
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Rebellion and Splintered Core
Many vehemently protested the new measures of donning the biohazard suits, as they deem such actions as discriminatory and a subjugation of their mutant identities.
A silly reason to revolt. Who wants to die horribly for lack of readily available protection?
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Instead of biohazard suits, the protesters suggested that the Combine redirected all its resources towards a two pronged strategy: (1) connect all existing airtight residential vaults called biodomes
Way beyond the technological means of a few million people.
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with a network of tunnels; and (2) accelerate the development of a vaccine that was supposed to have been completed years ago.
Completely pointless, see above.
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The first measure was agreed by many (even amongst the Pure Men) as the most viable strategy, which made the rejection from the high council raise even more questions and conspiracy theories. Despite the rare joint protests of all mutant groups (including many Pure Men as well), the high council instead sent riot control police to suppress their dissenting voices, resulting in unnecessary bloodshed over the course of two weeks.
Skip the second epidemic and cut to the riot police as soon as there are, uh, riots. We are talking about an evil totalitarian government with some hidden agenda, they are supposed to be heavy-handed.
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This dissatisfaction quickly led to the formation of two splinter groups; with one preferring to leave the Combine in peace and the other choosing a more violent route.
Those who left the Combine traveled north and eventually settled down in Oasis. They eventually merged with the Lorekeepers whose sole objective in life is to rediscover pre-desertion knowledge, forming a semi-religious order known as the Awakened Order.
Sudden introduction of an unnecessary entity.
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Those who chose to resist the Combine's new law with violent means escaped into the underground tunnels
What underground tunnels?
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beneath the Combine cities and called this new home the Gloomy Tunnels, from where they plotted rebellions against the government. In honor of the first mutant who was executed for refusing to put on the biohazard suit, they called themselves the Saberions after her maiden name Sabari.
It is during this time that the protagonist is born, in a quiet little village in Oasis called Moonstone.