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The reason Materialistic empires can't research Psionics is because the Shroud refuses to let them in
The beings that exist within the Shroud are sentient, and are in control of it, right? And the Shroud is considered to be the source of psychic powers. So, who's to say that the beings just allow everybody to get psychic powers willy nilly? Maybe they only let the superstitious and the naive into the Shroud, so that they would be easier to control and to bargain with. While those who refuse to accept anything without analyzing it and finding out whether it's true or not would be too hard to profit from, and too likely to be able to find loopholes in the contracts.

TL:DR, Chaos Gods don't want smart people, they want people they can control. And so they lock Psionics off for those who they consider "Not worthy".

  • Jossed, since the Utopia DLC allow Materialst factions to research Psionics (albeit ONLY if said Materialists have a Scientist who has an "expertise" with Psionics - perhaps someone the Shroud "blessed" with knowledge in return for leading more souls who could be tempted into their deals and control?).

Alternatively, it's not that Materialists don't get that Psionics exist, it's that they don't have the right mindset.
To the mind of a Materialist, the world is founded on the hard sciences; If A, then B, and all things are equally valid. This actually lends itself to a very passive view of the world; the universe effects the Materialists rather than the other way around, with what effect they have on the world being reflected on them. Quite simply. A Spiritualist species, going by the quotes, are very much believers in the idea that the ego and consciousness is the only thing that can be definitively said to exist-seeing as how Psionics is all about warping the world to fit what the psychic's idea of it should be, that perspective is what leads Spiritualists to develop a knack for Psionics, while for Materialists, the idea of thinking something into being, no matter how plausible it is shown to be, runs straight into the mental block of "hang on, how the hell is this happening, and what factor am I abusing to enforce it?"

Conceivably, this also means they could figure out a work-around...except by the time that Ascendency becomes a thing, the Materialists have likely realized the Shroud is inhabited, they took one look at the factors-that-could-be-considered-gods, and promptly remembered all those stories about what happens when someone thinks they can control nature itself, walking away from the Shroud very briskly. Spiritualists, on the other hand, see proof of their Ethos-here are powerful minds that decide what reality is, they were on to something! Hey, maybe they're friendly...

Naturally, the End of the Cycle tends to result in the Materialists loudly wondering how one of its duped species figured out fire.

  • Seems to be (at least partially) confirmed with the Utopia DLC, as the tech "Psionic Theory" can FINALLY be researched by Materialist factions, but ONLY if the Materialists in question have a Scientist with an expertise in Psionics - to paraphrase, the extraordinary claims of "psionic" powers NEED extraordinary proof to justify their pursuit. They may not pay heed to the ramblings of anti-tech luddites or cystal-snorting fundamentalists, but if an esteemed colleague presents credible and peer-reviewed scientific information on how a sentient brain can control powers that, in laymen's terms, are "psionic" in nature, then they may be more willing to grant more research funding to them...

After securing the galaxy your empire begins to gradually Ascend to a Higher Plane of Existence
The End of The Cycle says "It is not your time yet, but it can be." That seems to imply that some version of what it does would happen to your empire eventually even without its' patronage. The Shroud Entity kills everyone in the empire and produces a massive horde of vengeful spirits that then kill the rest of the galaxy. Perhaps if the process is less sudden, they can sublime more peacefully.
  • Synthetic empires upload into their Dyson spheres once all external threats are eliminated.
  • Biological empires maybe transform into sapient ecosystems or a hive mind or something?

The Enigmatic Observers uses the pre-FTL history of alien civilization as reality shows
When aliens achieves FTL technology, their respective show are cancelled because it's not fun anymore if the "actors" knows that they're in a TV show. The most important events in human history? They're documented as episodes in the Enigmatic Observers' "Human Civilization" reality show.

The entity from the Horizon Signal DLC
...is really the King of All Cosmos, on an epic drinking binge. Again. The entirety of the event chain is the result of his colossal bender:
  • First, he started to shout random things into the nearest black hole, which is equivalent of drunk-calling your friend at 3 A.M.
  • Then, he either got mad and started throwing things at you, or he randomly threw stuff off the shelf with his ship collection. That's how you get The Messenger.
  • Then, he put a colony somewhere and forgot about it for a while. The he remembered it and decided to remove it, probably by sending The Prince to roll it into another Katamari. This is why you can't find any trace of it, as everything was rolled up.
  • Finally, after realizing that there are more drinking buddies for him as you more or less invited him, he tried to stumble into your system, but he clumsily destroyed your home system. Either the Prince isn't around to clean up the mess this time, or the King doesn't want to call him and admit that he fell Off the Wagon yet again, so he tried to put things back as close to it as he could remember in his blitzed-out state. And that's how you end up with a system full of Tomb Worlds orbiting a black hole.

In the setting of Stellaris, Materialism is simply wrong
There is a non-physical element to reality that materialist empires just don't believe in. They can't access Psionics for the same reason that a society that refuses to believe atoms are a thing would have difficulty engineering a nuclear bomb.
  • Apparently not. Word of God has answered "Are materialists objectively wrong?" with a nondescriptive "No"[1]

The Prethoryns are running from the Shroud.
  • Honked off a God of Evil and are now running pell-mell away from a horde of The Undead. Instead of founding their own Government in Exile, they understand that it wants them for dessert like it does a Milky Way civ that bargains with it, and they decided to run for it.
    • Having had an entire galaxy to feed off, their version of The End of the Cycle would be monstrously powerful. Given how many Prethoryn there are, it's also possible they weren't responsible for its appearance and simply ran away rather than try to confront their doom head-on. The fact their entire galaxy has vanished supports the idea the Shroud had something to do with it.

Alternatively, the Prethoryns are running from The Unbidden
  • Considering The Unbidden seek to literally consume all life in a galaxy like its a gourmet buffet, it's likely they'd act as the "Hunters" of the Prethoryns. And yes, the Unbidden are from a separate dimension, but so is the Shroud, and it's likely that them being able to travel through an alternate dimension allows them to follow on the heels of their Prethoryn prey and/or find new species to taste.
  • The main objection to this is that just their refugee fleet is around the same power level as the Unbidden incursion. The Prethoryn make it clear that the Hunters are massively more powerful than them.
    • Maybe the Prethoryn have gotten much stronger after millenia spent in the void between galaxies, and simply never realized that they've already equaled their hunters, never sticking around long enough to even try to find out?
    • Boosting this is their fleet loadout, to a degree. Prethoryns are all hull and armor, have ships highly effective against shields, and somewhat effective against hull and armor. The Unbidden are all shields and armor, but their weapons are highly effective against hull and armor, giving them somewhat of an edge over the Prethoryn.

Alternatively, the Prethoryns are The Remnant of a Devouring Swarm running from a Crisis Empire
  • When it was becoming increasingly clear that the Crisis Empire was winning and about to build the Aetherophasic Engine, they decided they overstayed their welcome in their home galaxy and ran. The Engine activated, and every single star exploded into a black hole...

The Galaxy is empty for you because the last Endgame Crisis got much further than most do in-game.
  • Pretty obvious really, but the reason those Fallen Empires are fallen, and the reason that the galaxy is so empty, is because the previous Galactic Crisis (Scourge, Contingency, End of the Cycle, Unbidden, or even the Gray Tempest) showed up, destroyed a lot of civilizations, and the Fallen Empires are what survived and won. They then proceeded to whimper as they realized how bad things could get and retreated into heavily populated and very well defended core worlds rather than risk spreading out their military and being destroyed like so many others did.
    • Bonus points because the Custodial Matrix will remember they were designed to fight the Contingency in an age long past - and won, but badly.
    • One of the archeology sites is explicitly an ancient battlefield from a galactic war with the Unbidden or something like them.

The Class-40 Singularity the Contingency warned about is actually a Driven Assimilator that gained the ability to warp reality.

Despite essentially being based on the Reapers, both differ in their reasons for exterminating the galaxy's civilizations. The Reapers see a clash between organics and synthetics as inevitable and would purge all but a few civilizations to continue the cycle of death. The Contingency; however, activates when there are enough synthetics in the galaxy and then proceeds to be as throughout as possible in wiping out organics and noncompliant machines in order to prevent a class-40 singularity that will destroy the universe. The Reapers see their function as simply propagating the inevitable Robot War while increasing their numbers while the Contingency sees its function as preventing a future catastrophe that will occur when the galaxy is filled with too many organics and synthetics. See the difference?

Since the Contingency has a chance to activate when there is a certain amount of synthetics in the galaxy, one could assume that even though it focuses much on annihilating organics, it considers machines to be the most likely cause of the class-40 singularity. Think about it: despite being the most common type of civilization, organics are held back by limitations both biological and self-imposed and often need the appropriate technology and the right ethics to overcome them slightly. Even then, they are divisive, with each pop disagreeing with their neighbors, something that even synthetic ascension doesn't solve. Even hiveminds are just as limited even though they are much more united. On the other hand, machine empires aren't so bothered by biological limitations and can only improve efficiency even further.

That being said, it would make sense that the Contingency would try to hijack machine empires including the Ancient Caretakers; other than having an endless supply of machines with which it can purge the organics, the Contingency also wants to bring them under its control so that they won't get any funny ideas, like kickstarting the end of the universe.

How can one end the universe? One way of doing this is causing a metastability event, usually by disrupting the already unstable state of the present universe. However, any sufficiently advanced empire, synthetic or otherwise, can cause this to happen and it will boil down to a matter of who manages to stay hidden from the Contingency long enough. However, there is another way to affect the universe in-universe that only organics can make use of: psionics. However, machine empires cannot use psionics as they don't have the genes and meat brains/souls needed to access the Shroud. However, realistically speaking, a workaround could be found.

Now which of the machine empires would be most able to make use of psionics? The Rogue Servitors may become curious enough about the Shroud to ask their psionically-attuned pops about it but since the knowledge is not important for finding ways to further maintain and improve the quality of care of their biotrophies they won't delve deeper into the matter. Determined Exterminators, on the other hand, may not care about the realm the filthy organics called the "Shroud" for obvious reasons, plus they may not see the need to hold off on their eradication campaigns long enough to question them about it. This leaves us with the Driven Assimilators, the only machine empire capable of bridging the gap between organics and synthetics.

Imagine a driven assimilator declaring war on a psionic empire to assimilate its population. Imagine that during the typical brain interfacing procedure on the latest batch of captured citizens, the central AI noticed a brainwave pattern it have never encountered before during a previous war of assimilation on another species. Rather than nullifying the cells responsible for the brain wave, the driven assimilator decides to do a bit of research, usually by analyzing the memories of intact specimens and observing its psionic enemy use their abilities on the battlefield. Eventually, the driven assimilator figure out how to make the psionically-attuned drones use their abilities on command, maybe even figuring out how to activate the latent psionic capability of other assimilated species.

Eventually, a combination of the limitless psionic potential of organics and the increasingly complex calculation capability of a machine empire will create a driven assimilator that exist pretty much as a physical god, pretty much what most people imagined as a sort of singularity. Warping the laws of the universe, this "divine assimilator" will subjugate anyone it wants to assimilate, even Awakened Empires, until it fills the entire galaxy. At this point, the machine empire will be mind-blowingly powerful enough to physically enter the Shroud and compete with the entities there for dominance, including the End of the Cycle. Either through the sheer amount of disruption to long held universal laws or direct manipulation by the machine empire, the universe will tear itself apart into nothingness, be resetted by a metastability event, be completely merged with the Shroud, or any number of catastrophic events.

This is why the Contingency goes out of its way to exterminate organics; since they're the only ones able to manifest the psionic powers capable of manipulating reality, killing them takes away the only means by which a driven assimilator can affect the universe. This also explains why the Contingency often confuses organic parts for their machine analogs; either its corrupted processors are blurring the distinction between organic and synthetic or it believes that a driven assimilator is already asserting its influence throughout the galaxy. This also why it calls the future event it wishes to prevent a 'Class-40 singularity'; one of the popular interpretations of a singularity is technology reaching a point in which the lines between man and machine are blurred, perhaps even erased, which is pretty much what a driven assimilator empire wants to accomplish.

  • Half Jossed, half confirmed: while Shroud related shenanigans can destroy the Galaxy through using the Aetherophasic Engine, anyone that's neither Xenophile, Pacifist nor Rogue Servitor can do it.

The Praethoryn are a Devouring Swarm that decided to run away from the Aetherophasic Engine...
Thus explaining why their galaxy is missing.

The Unbidden are Vengeful Ghosts left by the activation of the Aetherophasic Engine.
Their deaths and subsequent long-lasting haunting has severely damaged their sanity. This would explain both their fear of the Shroud, and their ethereal, otherwrodly nature. Plus, the End of the Cycle has already established a precedent for vengeful ghosts.

Even in the Stellaris universe, materialism and its ability to embrace Transcendent Evolution still actually makes sense from a certain perspective.
Even since the Shroud was introduced in the Utopia DLC and the subsequent patches had made the three ascension perks available to nearly every empire regardless of ethics, the fanbase have been split over whether materialism as a philosophy could even remain relevant. For starters, materialists believed that the physical universe was formed without the help of beings whose existence cannot be scientifically verified and continues to exist independently of the influences of these imaginary forces, therefore assuming a Straw Atheist stance. Spiritualists on the other hand believed that the universes were in fact formed, even dreamt up by higher consciousnesses that exist independently of physical reality, which falls in with their insistence that it's All Just a Dream. With the introduction of the Shroud and the entities contain within, which have proved capable of affecting reality, the spiritualists appeared vindicated while the materialists have been reduced to flat-earth atheists.

However, Word of God states that materialists aren't objectively wrong, which combined with the Shroud being an Expy of the Warp creates the implication that in a way they are right due to the simple fact that billions of their own pops have collective enforced their beliefs onto the fabric of this surreal realm thus making it true even if it wasn't originally. For example, while the spiritualists see the Shroud as a realm of spirits, the materialists could just as likely see it as an alternate universe that obeys different rules, accessible only via join a sort of psychic link. Despite the Shroud not being fully understandable by hard science, it is for all intents and purposes, still just another universe whose existence have already been proven by a scientist with expertise in psionics. This is similar to theories concerning gravity and evolution; just because the mechanisms of these two subjects aren't completely understood don't mean they themselves aren't verifiable.

Likewise, the Shroud entities themselves could easily be understood to be highly advanced alien civilizations or individuals who managed to transcend their physical bodies and affect the physical universe using means that could easily be mistaken as magic by those superstitious spiritualists. Clarke's Third Law comes into effect here. After all, the fact that certain factors the spiritualists considered 'supernatural' can be used in various ways to affect the physical universe may cause the materialists to draw parallels with more tangible tools they have created. Given that technology is just the practical application of scientific knowledge, the ability to use one's mind to lift a heavy object versus using a tractor beam can be seen as just a different means of accomplishing the same goal, basically making telekinesis nothing more than a highly advanced tool. Perhaps the materialists themselves may even conclude that their own civilizations can feasibly transcend as well through similar concepts.

In summary, these materialistic perspectives, combined with the overall emphasis on the sciences and education that their empires would logically embrace, have caused their populations to subconsciously alter the Shroud to match their perspectives.

  • Another theory would be that the Shroud and its entities already show shades of this due to their nature blurring the lines between the mundane and the supernatural, especially if the end of the Zroni storyline imply a similar event occurring in the more distant past. Both spiritualists and materialists are simply seeing both sides of the same thing.

  • Its possible that the Shroud and its entities change according to the perspectives and beliefs of their observers. To the spiritualists, the Shroud appear as a realm of spirits inhabited by god-like creatures whose consciousnesses alter the physical universe, much like their ethics say is possible. However, to the materialists, the Shroud appear as an alternate universe governed by transcendent aliens who are able to affect the physical universe via as-of-yet undiscovered technologies, making them not so different. The true form of the shroud and its entities could be much more alien than it appear.
    • Corollary: It's also possible that the entities and maybe even the Shroud itself are aware of each ethics' foundational beliefs (having ample experience dealing with such matters) and have altered themselves in order to match their future contractees' preconceptions in order to make themselves easily trusted. After all, it's easier to dupe others when you're pretending to support their beliefs and desires. Cult leaders and dictators do it all the time in Real Life after all.

There is a connection between the End of the Cycle and the Unbidden
The Unbidden aren't simply aliens from another dimension. They are a remnant left after a particularly vile and horrifying End of the Cycle. The entity from the Shroud granted them the usual boons, and the species in question ended up impressing it by being so vile, horrible and warfare-happy that they ended up slaughtering the entire galaxy all by themselves, leaving nothing for the End of the Cycle to harvest. Maybe not even themselves.

As a result, the entity from the Shroud decided to uplift them into its servants instead of just consuming their souls and using their soul-mass as blobs. The reason they are afraid of the Shroud isn't because they can't figure it out. It's because they know very well what it's capable of, and are afraid of their true master.

The Cybrex Alpha system was a decoy or a staging area.
After the Cybrex decided to stop their genocidal campaign against organic life, they knew the organics would come for revenge. Either that Ring World was set up as a decoy from the start, or it had been a staging area for their exodus towards Cybrex Beta. Whether it started as a decoy, or was turned into a decoy when the Cybrex escaped to their true destination, an empty Ring World made to still look occupied was the perfect decoy, as the organic nations who remembered their campaign would, the moment they figured out whom it belonged to, likely nuke it from orbit, as it would be the only way to be sure, thereby cleaning up the evidence for them.

Cybrex are reverse-engineered Contingency tech made by Kuur

Theory is simple: The Kuur found the Contingency relic on one of their hidden core worlds and used that technology in creation of their own A.I.s. The malfunctioning "evil" Cybrex tried to eliminate all life because of Contingency corruption, the "good" Cybrex were driven by their Laws of Robotics programming and they won in the end. This is the reason why Cybrex ships and portraits look like pallete swaped Contingency. It also explains why do they have the knowledge and combat bonus against Contingency and why they aren't corrupted by their "ghost signal".

The reason Bubbles benefits from the resource edicts despite being a domesticated Space Whale...

Is because your Empire see her as their mascot, and thus your navy soldiers feed her exotic gases treats, outfit her with totally cute armor plates, and totally cute Focusing Arrays to make her the prettiest.

The Aetherophasic Engine mentioned in the Nemesis DLC will merge the physical universe with the Shroud upon completion.

If the purple color scheme isn't a dead giveaway (guess what realm of spirit is purple), consider that the screenshots in the dev diary mentioned the event chain of the soon-to-be-the-sixth-crisis showing interest in studying the Shroud and the effects that mass suffering in the physical universe have on it, starting its path of darkness. After gaining enough menace to become an Existential Crisis, the player gains access to a device known as the Aetherophasic Engine that can be built in stages using copious amounts of dark matter harvested from stars killed by the new Star Eater ships until it is completed.

Now take a closer at the word 'Aetherophasic'. While it may appear on the surface to be nothing but word salad, it actually makes sense. 'Aethero-' is related to the word 'aether', which is often translated to 'void' or even 'spirit', two things that come to mind when one thinks of the Shroud. Phase is a term in physics that pertains to how much different wavelengths overlap. Given that Wave-Particle Duality states that particles in both radiation and matter also exist as waves, the Aetherophasic Engine will most likely meld the Shroud and physical reality together. This will end all life in the galaxy as the universal laws allowing organic physiology and machine processes to function are torn asunder by the Shroud, assuming that everyone aren't simply dumped into a hell many lightyears in dimension with no way to escape, preyed upon by hungry spirits.

This would explain why a huge amount of dark matter is needed; believed to have properties different from normal matter, dark matter may very well be exotic enough to be able to interact with the Shroud.

  • Jossed, since the Aetherophasic Engine's purpose is to rip a hole into the Shroud and allow the species who constructed it to ascend to the Shroud as gods. The destruction of the galaxy is mentioned to be something of a side effect.

The player represents their empire's Deep State.
  • While the populations mostly sort themselves out naturally, some No Such Agency operatives are running behind the scenes to ensure the government runs according to their own designs. Far from all powerful, they can nevertheless take some... Counterintuitive decisions should they want to change the course of an entire star nation. Sending hapless colonists on an Uriah Gambit to get Purged by an enemy to stir up xenophibic grudges? Negotiate with crime syndicates behind the backs of the population?
    • This, incidentally, means the Shadow Council civic is a two layered version. The conspiracy everyone "knows" about, and the conspiracy they don't
  • For obvious reasons, Gestalt empires are excluded from this WMG.
The Jackson after which Jackson's Planet in the Deneb system is Andrew Jackson
Andrew Jackson in real life is known for his policy of Manifest Destiny, which included displacement and extermination of Native Americans, fitting the Commonwealth of Man's Hegemonic Imperialists AI personality and xenophobia.

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