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Easter eggs

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This article is timeless and should be accurate for any version of the game.
Why? Why?! WHY?! - Embracing the futility of life's questions in the Improbable Ceramics event
My circuits hurt. - Same option for machine empires

Easter eggs are inside jokes and references to popular culture, included for the player's amusement. This is a non-exhaustive list of Easter eggs present in Stellaris. For others, also see the TVTropes page.

Contents

The Blorg

During the pre-release stream series former Stellaris game director Wiz was inspired by one of the fungoid portraits to create a very friendly but hideously ugly species called the Blorg. The Blorg Commonality was a fanatic xenophile misunderstood empire that desperately wanted to make friends, and also had a militarist side in order to force others to be their friends if everyone rejected them. Due to fan requests, the empire was included in the game at launch, together with the Fanatic Befrienders AI personality, unique only to the Blorg and any empire with the exact same ethics and traits.

The Blorg became something of an inside joke within the game. The xenophile advisor references to the Blorg as friendly, the Subdermal Stimulation tech shows a Blorg body-pillow, the Chemical Bliss drugs it unlocks include Blorg bodily fluids, and the Uncanny trait (which describes machines made in the image of one of the most horrific species in the universe) shows a robotic Blorg. Finally, a possible name for black hole systems is Blorg's Bane.

Species with the Blorg portrait have a 1 in 140 chance to say "Umm...friends?" instead of regular fungoid sounds when contacted via the Contacts menu.

War in Heaven

Named after a biblical event from the Book of Revelation, the name also refers to the Second Shadow War in the series Babylon 5. Humanity is caught in the the middle of a war between two ancient forces: the awakened Shadows and their ancient rival - the Vorlon Empire. Humanity led the Army of Light opposing both ancients, by allying with the League of Non-Aligned Worlds and the Minbari Federation.

The achievement   Last, Best Hope also refers to a line repeatedly said within the show that the eponymous station was the last, best hope for peace, and formed the aforementioned League of Non-Aligned Worlds. The achievement requires leading the said league to victory against both Awakened Empires.

When a Fallen Empire awakens the dialogue box also repeats a line from the series: Giants in the playground....

The Hitchhiker's Guide to the Galaxy

Stellaris contains a number of references to the Hitchhiker's Guide to the Galaxy novel series. More importantly though, the actual series is present in the game. One of the anomaly events from the   Distant Stars DLC called Honeymooners leads to the discovery of the "alien travel guide", identically named The Hitchhiker's Guide to the Galaxy, which supposedly describes "many sights and phenomena still unknown to us".    Xenophile and    Xenophobe empires can use it to boost their respective ethics' attraction for 10 years.

One of the unique systems from   Distant Stars contains a species called Prikki-Ti, which is sealed on their Shielded world inside a time warp and will become a Fanatic Purifier empire if they manage to get out alone or with player intervention. They are a reference to the Krikkit species from the third novel, which fails to exterminate all other life in the galaxy and gets sealed that way.

If Earth is shattered with a World Cracker there is a 50% chance of creating a wormhole in the system leading to another newly created wormhole, something that also happens in the novels.

Ringworld Homage

The Sanctuary system, containing a ringworld populated by primitive species that was designed by a precursor empire to house and preserve primitive life, is a homage to Larry Niven's Ringworld, the novel which is the origin of ringworlds concept in fiction.

While constructing a ringworld another empire might contact you thinking that you are making weapons of mass destruction on your ringworld, a reference to the titular ringworlds from the Halo series.

Civics

The governments and backgrounds the civics generate also match the referenced series.

  Citizen Service

Reference to Terran Federation from the Starship Troopers series.

  Imperial Cult

Reference to Warhammer 40k.

  Fanatic Purifiers

Reference to Warhammer 40k, complete with descriptions and dialogues common in the series.

  Devouring Swarm

Reference to the Tyranids from Warhammer 40k and the Zerg from StarCraft.

  Driven Assimilator

Reference to the Borg from Star Trek.

  Determined Exterminator

Reference to Skynet from Terminator. In the game files the civic is even called terminator.

  Rogue Servitor

Reference to the Minds from Iain M. Banks' The Culture.

Traditions

  To Boldly Go

Reference to the main premise of Star Trek

  Standard Construction Templates

Reference to Warhammer 40k

Armies

  Clone armies

Reference to the Star Wars prequel trilogy.

  Xenomorph armies

Reference to the Alien franchise.

  Gene warrior armies

Reference to the Space Marines from Warhammer 40k. The technology unlocking it is also identical.

Planetary Features

  Underground Vault

Reference to the vaults from Fallout

  Portal Research Area

Reference to Doom series

Traits

  Nerve Stapled

Reference to Sid Meier’s Alpha Centauri

  Proles

Reference to most of the population from George Orwell's Nineteen Eighty-Four

  Towel-bearer

Reference to the first rule of Hitchhiker's Guide to the Galaxy. The event giving the trait is appropriately named Stay Calm.

  Hell's Heart

Reference to the Moby-Dick novel

Strategic Resources

  Living Metal

Reference to the Necrodermis from Warhammer 40k

  Zro

Reference to Element Zero from Mass Effect

Species

  Second humanoid species

Reference to the Klingons from Star Trek

  Fifth humanoid species

Reference to the Vulcans from Star Trek

  Fourth humanoid species

Reference to the alien character Diva Plavalaguna from The Fifth Element

  Fox mammalian species

Reference to the Star Fox series

  Fifth Reptilian species

Refrence to Kowakian Monkey-lizards from Star Wars

  Fifth molluscoid species

Reference to the Yahg from Mass Effect

  Creatures of the Void arthropoid species

Reference to the Shadows from Babylon 5

  Space suit avian species

Reference to the Psycrows from Earthworm Jim

  Chirpy avian species

Reference to the social media logo from Cities:Skylines

  Mammalian-inspired machine species

Reference to Andromedons from XCOM 2

  Droid (second tier robot)

Reference to Star Wars, where all robots are referred to by this term (a contraction of "android")
Humanoids Species Pack
Half of the portraits from the species pack are inspired after common fantasy races

Flags

  14th human flag

Reference to the United Federation of Planets from Star Trek

  13th human flag

Reference to the Crux Terminatus badge from Warhammer 40k

  2nd domination flag

Reference to the Terran Empire from the Star Trek mirror universe

  22th round flag

Resembles the Mantle of Responsibility mark from Halo

Achievements

  Brave New World

Reference to Aldous Huxley's dystopian novel of the same name

  Emissary

Reference to Star Trek: Deep Space Nine

  Clever Girl

Reference to a famous line from Jurassic Park

  Deus Vult

The Christian motto from the First Crusade and a common line in Crusader Kings II

  Domo Arigato

Reference to the 80's song Domo Arigato Mr. Roboto by Styx

  Power Overwhelming

Reference to the invulnerablity cheat code and archon quotes from the StarCraft series

  Faster, Stronger, Better

Reference to the TV series The Six Million Dollar Man

  Voight-Kampff

Reference to Do Androids Dream of Electric Sheep

  Break on Through

Reference to The Door's song Break On Through (To the Other Side)

  ...To the other side

Reference to The Door's song Break On Through (To the Other Side)

  Building Better Worlds

Reference to the Weyland Yutani company motto from Aliens which specialized in terraforming and space exploration

  Suffer not the Alien

Reference to the motto of Deathwatch who excels in fighting xeno threats for the Imperium of Man in Warhammer 40k.

  Payback

Reference to the 2009 TV series "V". The achievement picture is an also an inverted version of the series' poster.

  Then Virgil, Now Beatrice

Reference to Dante's Divine Comedy

  1999AD

Most likely a reference to the 1995 JRPG Chrono Trigger as in that game a creature named Lavos falls from space and burrows down into the planet's core in the prehistoric age where it grows in size over many millennia before emerging again in the year 1999AD, destroying the planet as it does so.

  Outside Context

Reference to the Iain M. Banks book Excession. The author coined the term "Outside Context Problem" to indicate a surprising and unexpected situation, such as an invasion by massively superior alien force occuring in the middle of World War 2.

  Like Tears in Rain

The title of this achievement references the famous monologue of Roy Batty from the film The Blade Runner. The subtext is (also) a nod to the System Shock series of games where the main Antagonist is comparing pathetic creatures of meat and bone with itself.

  I Can See Forever

Reference to the works of H.P. Lovecraft and his Cthulhu Mythos

  Rise of the Machines

Reference to Terminator 3: Rise of the Machines

  Planet of the Mechs

Reference to the Planet of the Apes series.

  Distinctiveness Added

Reference to the Borg from Star Trek

  Exterminatus

Reference to the famous course of action in Warhammer 40k

  Pandora's World

Reference to Pandora's Box from Greek mythology. Lowering the shield also brings similarly bad results.

  Stay on Target

Reference to Star Wars Episode IV

Slavery Types

Battle Thralls
Reference to the Ur-Quan Masters from the Star Control series
Grid Amalgamation
Reference to the Matrix series. In the game files the slavery type is even called matrix.

Endgame Crises

The Contingency
Reference to the Reaper cycle from Mass Effect.
Extradimensional Invaders
Reference to the Devidians from Star Trek: The Next Generation.
The Prethoryn Scourge
Reference to the Tyranids from Warhammer 40k or Yuuzhan Vong from Star Wars.
The Reckoning
Reference to the Fall of the Eldar in Warhammer 40k.

Ship names

The standard human namelist used by the United Nations of Earth is loaded with references; for instance, all Destroyers are named after cities, whilst Cruisers are named after battles (Somme, Hastings, Bunker Hill) and military commanders/leaders (Julius Caesar, De Gaulle, Genghis Khan), construction ships are named for oceans and rivers (Pacific, Atlantic, Volga, Ganges, Rhine), science ships are named for explorers and scientists (Grissom, Gagarin, Asimov, Hawking), and so on.

Enterprise (battleship)
Reference to Star Trek.
Firefly (corvette)
Reference to Firefly, the main ship's class.
Greased Lightning (corvette)
Reference to the cult movie Grease.
Serenity (colonizer)
Reference to Firefly, the main ship's name.
Thunder Child (destroyer)
Reference to War of the Worlds.
Yeager
Reference to Chuck Yeager, the first person to travel past the speed of sound

Pirate ship names

Aside from pop culture references, many pirate ship names are reminiscent of the naming conventions of Culture starships, from Iain M. Banks' fictional setting.

The Slings, The Arrows, and Outrageous Fortune
Reference to Hamlet
Black Earl
Reference to the Pirates of the Caribbean series.
Attack on Freighter
Reference to Attack on Titan
Tycho, Durandal, Leela
Reference to Marathon, the eponymous colony ship's three shipboard AIs.
Oh, That's a Pirate!
Reference to a video game in Part 3 of JoJo's Bizarre Adventure.
Soylent Green
Reference to the movie Soylent Green.
Resonance Cascade
Reference to Half Life.
Hell's Bells
Reference to the Hells Bells song by AC/DC.
Pillage and Reconciliation
Reference to the ship "Truth and Reconciliation" from the popular video game Halo: Combat Evolved
Comet Sighted!
Reference to the "Comet Sighted" event.

System names

Real

There are almost 200 real star names provided in Stellaris as potential random names for solar systems. Here are the ones that also have significance in the media:
Algol system
Perhaps better known as Beta Persei. Also features in the Phantasy Star series.
Alpha Centauri system
Our closest neighbor; always spawns near Sol. Featured in a great many books, movies and games.
Antares system
One of the real star names present in the game. Reference to the Antares system from which the Antarans launch their attacks in Master of Orion 2: Battle at Antares
Beta Corvi
The second brightest star in the southern constellation Corvus (the raven). In Star Control II, Beta Corvi IV is the gas giant home of the Slylandro, who share some similarities with Stellaris' Dathnak.
Epsilon Eridani
A real system approximately 10ly away, and in the Halo series, a Human stronghold system - home to the fortress world Reach.
Gamma Draconis system
Also known as Eltanin, and features heavily in Freespace 2, as the discovery of an ancient jumpnode-stabilizing 'Knossos' device leads to a second war with the omnicidal, star-destroying Shivans.
Omicron Persei
Though it is a real star system it is likely also a reference to "Futurama" where the overlord Lrrr of the Omicronians lives on Omicron Persei VIII. If the system is big enough in Stellaris, there might just be an Omicron Persei VIII.
Rasalhague
Also known as Alpha Ophiuchi, part of a binary system. Features in the Battletech setting.
Rukbat
Also known as Alpha Sagittarii, setting of The Dragonriders of Pern series by Anne McCafferey
Sheliak system
Also known as Beta Lyrae, and a reference to a species of the same name in the Star Trek: The Next Generation.
Tau Ceti
A real star system and one of the closest to Sol in reality. Referenced in numerous books and shows, the most well known likely Star Trek. Also the destination of the starship Von Braun in the video game System Shock 2.
Trappist system
A custom predesigned unique system, resembling the TRAPPIST-1 solar system, which was discovered to have three exoplanets in 2015. In 2017, it was announced that four more exoplanets had been detected. The Trappist system always has an m-class star, a molten world, a barren world, a toxic world, a desert world, a continental world, an arctic world, and a frozen world, in that order.
Polaris
Also known as the North Star.

Fictional

There are another almost 1,200 fictional star names, many are completely fictional and unique to Stellaris, whilst others are pop-culture references or nods to the development team/community.
Alderaan, Dressel, Jabba and Lando
All are planet or individual names from Star Wars
Amlitzer
Reference to the battle in the Amlitzer system in the Legends of the Galactic Heroes
Arrakis
Reference to the arid planet in Dune's saga
Astarte
Reference to the battle in the Astarte system in the Legends of the Galactic Heroes.
Cknoor
Reference to the nickname of Anders "cKnoor" Carlsson, Streaming Producer at Paradox.
Covfefe
Reference to the meme that resulted from the misspelling of coverage in a tweet from American President Donald Trump
Eye of Hawking
Black hole system and tribute to theoretical physicist Stephen Hawking, the name was added in the first patch after his death. He famously proved theoretically that black holes could lose mass over time.
Giedi
Reference to the homeworld of House Harkonnen in Dune's saga.
Heaven's Gate
Reference to Heaven's Gate, an American UFO religious millenarian group.
Higashik-Ata
Reference to Part 4 of JoJo's Bizarre Adventure, Diamond is Unbreakable; protagonist's last name.
Kazon
Reference to the Kazon tribes, an aggressive and sectarian species from Star Trek Voyager. Dogar and Kazon are also the twin gods of Evil and Darkness in Star Control II: The Ur-Quan Masters.
Kazoo
Reference to the kazoo of cKnoor, as seen in the pre-release stream.
Kerbol
Reference to the central star from Kerbal Space Program
Kuma
Reference to the nickname of Björn "Kuma-kun" Iversen, Audio Director at Paradox.
Mar-Adetta
Reference to the Battle of Marr-Adetta in "Legend of the Galactic Heroes".
Manward
Reference to the Game Director of Stellaris, Martin Anward.
Olimar
Reference to the protagonist of Pikmin.
Polgara
Reference to the sorceress Polgara of the Belgariad series.
Rantemario
Another reference to a star system in the Legends of the Galactic Heroes.
Tantanga
Reference to the alien invader from Super Mario Land.
Targon
Reference to Mount Targon from the League of Legends lore.
Tiamat
Named after a goddess from the Babylonian pantheon, it appears as an item or creature name in Dungeons & Dragons and a number of video games.
Ulm
Reference to a small German one province minor in the Europa Universalis series, another grand strategy game by Paradox.
Vermillion
Another reference to a star system in the Legends of the Galactic Heroes.
Vohaul
Reference to the villain Sludge Vohaul in the Space Quest games.
Yildun
Reference to the headquarters of Technodyne Industries of Yildun in the Honor Harrington novels.
Yump
A reference/joke at the expense of Game Director Martin "Wiz" Anward, for his repeated (mis)pronunciation of 'jump' as 'yump' (in relation to FTL travel) during prerelease livestreams. In the random name list (/common/random_names/base/00_random_names.txt), it appears directly below 'Kazoo' and 'cKnoor'.

Planet names

Alpha Complex (Ring World)
The name of the facility the tabletop RPG "Paranoia" takes place in; which is also taken care of by a Custodian Matrix.
Dune (desert world)
Another name for Arrakis from Frank Herbert's Dune saga.
Kipling (jungle world)
Reference to Rudyard Kipling, an author famous for The Jungle Book.
R'lyeh (ocean world)
Reference to the sunken city from the Cthulhu Mythos by H.P. Lovecraft.
Dagon (ocean world)
Reference to the ocean-dwelling deity from a short story by H.P. Lovecraft.
Walled Garden (gaia world)
Translation of Rannoch, the Quarian homeworld's name from Khelish, their language, in Mass Effect.
Melpomenia
Reference to one of the Spatian's worlds in Isaac Asimov's Foundation Cycle.
Solaria
Reference to Isaac Asimov's Foundation series.

Asteroids

1337- prefix
An asteroid may get the random name 1337, which means "Leet" (elite) in leetspeak, a type of computer and Internet slang.
AT-, R2-, C- prefixes, and -AT, -ST, -D2, -3PO suffixes
All references to Star Wars.
THX- prefix and -1138 suffix
Reference to George Lucas' first movie, THX-1138. This name would appear several times in other movies made by Lucas, usually in the background or as subtle references in dialogue.
HAL- prefix and -9000 suffix
Reference to HAL in "2001: A Space Odyssey"
TLDR- prefix
Relatively common internet slang; stands for "Too Long, Didn't Read".
UL1M- prefix
Might be a reference to the EU4 state of Ulm.
OD1N- prefix
Odin, of Norse Mythology.
VIR- prefix
Likely a nod to the tutorial AI, VIR, and possibly Vir Cotto of Babylon 5.
WPR- prefix
Possible reference to WOPR, the military supercomputer antagonist of the 1983 film WarGames.
LV- Prefix
Reference to LV-426 from Alien

Random events

Comet sighted
An event present in most other Paradox games
Anti-Alien Task Force
Reference to the XCOM and UFO series
Rogue Agent
Reference to James Cameron's Avatar
Eddic, Monolithic
Reference to Arthur C. Clarke's Space Odyssey
The Tree
Reference to the iconic scene from The Fountain
A Species of Ice and Ice
Reference to A Song of Ice and Fire
Glancing Hit
Reference to Mass Effect 2 dialogue about Sir Isaac Newton and the dangers of kinetic weapons missing their target, and subsequently traveling as long as required until they hit something.
Nimkip
Reference to Pikmin, a video game developed by Nintendo.
Improbable Ceramics
Reference to Russell's teapot, a philosophical analogy about the burden of proof.
Purple Rain
Reference to the song Purple Rain by Prince
Olfactory Study
Reference to Futurama's "Smell-O-Scope", the subsequent event "A Whiff of Something" explains it allows the user to observe "a collection of fairly short [comedic] narratives".
The Mysterious Moon
Reference to the Doom series
Horizon Signal
Reference to the movie Event Horizon
The Discovery of Alien Life
The Rogue Servitor response is "Wonderful! Prepare the gift baskets." which may be a reference to the film Pocahontas in which upon sighting the New World, Wiggins says "Oh, gift baskets!", after missing Governor Ratcliffe's insinuation they will kill the "savages".
The Gun Pointed at the Head of the Universe
Word-for-word title reference to a track from the first Halo's soundtrack. Appropriate, given the series' ringworlds are designed to unleash a Neutron Sweep-esque pulse to wipe out possible hosts for the Flood.
Broken Union
Reference to the Goa'uld from Stargate SG-1
Speed Demon
Reference to the endings of Mass Effect 3
MegaCorpse Concert
Reference to Metalocalypse. The player reply also references a memetic line from the series.

Messages

"The galaxy is dark and full of terrors."
Reference to the famous line from "Game of Thrones".
"Alert all commands. Deploy the fleet."
Reference to Star Wars Episode V.
"I can taste your stink and every time I do, I fear that I've somehow been infected by it."
Reference to Agent Smith from The Matrix.
"You will embrace the greater good, eventually."
Reference to the T'au Empire from Warhammer 40k. The reply is only available if your ethics match the T'au's (Authoritarian,Militarist,Xenophile)
"The spice must flow."
Reference to Dune.
"You are a rock tricked into thinking..."
Reference to a tweet by @daisyowl on the nature of computers.
"What a talentless looking [fox mammalian race]."
Reference to the Tails Gets Trolled webcomic.
"Make it so."
Reference to Jean-Luc Picard from Star Trek
"Look at the size of that thing!"
Reference to Star Wars Episode IV
"You may be wondering about the meaning of the mural behind us. That's a very good question with a very interesting answer! The price for the answer is 15 quadrillion Credits."
Reference to Star Control.
"The enclave is in a frisky mood. The creation of Scentilus Rift has caused many an artist to change their primary focus to creating new experiences for it."
Reference to Oculus Rift.
"May their reign stretch into infinity... and beyond!"
Reference to Toy Story.
"Well secluded, I see all."
Reference to The Rocky Horror Picture Show.
"Is Unit A5091-b in possession of a soul?"
Reference to the Geth question from Mass Effect.
"Brutal."
Reference to the Metalocalypse meme.

Diplomacy Messages

"Soon, communications from all your vessels will be blocked. None of you are free of sin." (Evangelizing Zealots negative greeting)
Reference to the Weird Twitter account @dril.
"The [Evangelizing Zealots ruler] Protects." (Evangelizing Zealots war greeting)
Reference to Warhammer 40k.
"This war will bring about an era of peace, justice, morality, culture, sport, family life, and the obliteration of all other life forms." (Fanatic Purifiers war greeting)
Reference to The Hitchhiker's Guide to the Galaxy.
"Please notice me senpai." (Fanatical Befrienders greeting)
Non-specific reference to Japanese anime.
"We are the [Hive Mind AI empire]. Lower your shields and surrender your ships." (Hive Mind war greeting)
Reference to the Borg from Star Trek.

Descriptions

"Some species are more equal than others." (Caste System citizenship)
Reference to George Orwell's Animal Farm
"Livestock is Pops!" (Livestock slavery)
Reference to Soylent Green
"Space is the final frontier" (Voidcraft technology field)
Reference to Star Trek
"There may come a time when intellects, vast and cool and unsympathetic, regard our worlds with envy and draw plans against us." (Planetary Defenses technology)
Reference to H. G. Wells' The War of the Worlds
"Where we're going, we won't need skin to feel!" (Subdermal Stimulation technology)
Reference to Event Horizon
"Let the enemy come to us. We shall fight them for every planet, every moon, every asteroid that lies within our space. We shall never surrender." (Defense in Depth war doctrine)
Reference to the second of Winston Churchill's three famous speeches
"We will add your biological and technological distinctiveness to our own. Your culture will adapt to service us." (Assimilation citizenship)
Reference to the Borg from Star Trek
"Glory to organics." (Bio-Trophy citizenship)
Reference to NieR: Automata
"Assuming direct control." (Machine Integration citizenship)
Reference to Harbinger from Mass Effect 2

Advisors

Militarist advisor
Reference to the Klingons from Star Trek
Spiritualist advisor
Reference to Babylon 5.
Xenophobic advisor
Reference to the Commisars from Warhammer 40k
VIR (tutorial advisor)
Click the portrait repeatedly for some funny comments, also a reference to Blizzard Entertainment games where units would have silly and often fourth-wall-breaking responses if clicked on multiple times in succession. VIR's name is possibly a reference to Vir Cotto from Babylon 5.
Diplomatic
Sample of diplomatic advisors voice, says "..and hot tea" wich is reference to Jean Luc Picard from Star Trek, who is diplomat as a captain of starship, an his favourite "Tea. Earl grey, hot"

Enigmatic Observers

The Enigmatic Observers have a tendency to lean against the fourth wall in their dialogue.

"All the world's a stage, and all the species are merely players. You are a player, are you not?"
Neutral greeting and a reference to William Shakespeare.
"Don't break the fourth wall, you clever child you."
Neutral greeting. Possible refrence to Clara Oswald from Doctor Who.
"You have ceased to amuse. Your little game will soon be over."
War greeting. Ironically they cannot give an empire game over unless awakened.

Leviathans

The Infinity Sphere & Gargantua
Reference to the Interstellar movie. One possible outcome causes the system to be renamed to Pantagruel, also making this a reference to the Gargantua and Pantagruel novel series. The damage modifier against it that can be obtained from the Curators is also a reference to Garrus Vakarian from the Mass Effect series.
Tiyanki Matriarch & AH4B
Reference to the Moby-Dick novel. The swallowed admiral is also coded to be humanoid if the DLC is installed.

The Shroud

The Shroud is modeled after the Warp from Warhammer 40k, and the Shroud entry dialogue contains plenty of references to various franchises.

Patron Entities

Composer of Strands
Inspired by the Chaos God Nurgle.
Eater of Worlds
Inspired by the Chaos God Khorne.
Instrument of Desire
Inspired by the Chaos God(dess) Slaanesh.
Whispers in the Void
Inspired by the Chaos God Tzeentch.

Entry Lines

"Do you think that is air you're breathing now?"
Reference to The Matrix.
"They should have sent a poet..."
Reference to the movie Contact. Itself referenced in Starcraft.
"Do you hear the voices too?"
Reference to the Chaos from Warhammer 40k: Dawn of War.
"Horror... horror has a face."
Quote from Apocalypse Now.
"What senses do we lack that we cannot see and cannot hear another world all around us?"
From the Orange Catholic Bible, also used in Dune.

Other

Crystalline Entities are Unbreakable special project
Reference to Part 4 of JoJo's Bizarre Adventure manga, Diamond is Unbreakable.
Despicable Neutrals (placeholder personality)
Reference to the people of the Neutral Planet in Futurama, and possible reference to the "Despicable Me" movie trilogy.
Mario and Luigi (the first two names in the Italian section of Humanoids 3 name list)
Reference to the main protagonists of Nintendo's flagship franchise
Zelda (female name from Humanoid 3 name list)
Reference to the title character from the Legend of Zelda series
Guardians of the Galaxy
Reference to the Marvel comic book series of the same name
Morphogenetic Field Mastery technology
Reference to the video game series Zero Escape, in which the the morphogenetic field is a plot point. The description also includes words cradle and pharmaceutical, a reference to the company Cradle Pharmaceuticals in the video game series.
Chinorr Stellar Union preset empire
A reference, albeit misspelled, to Paradox Studio's stream producer
Mharin Kharin Olfactory Arousal
Mharin Kharin is a reference to the Megami Tensei move Marin Karin which charmed/brainwashed enemies, and which has infamy among the fanbase for its inaccuracy and overuse by a character in Persona 3
  Machine Intelligence (no special civics)
Reference to the Geth from Mass Effect
L-Cluster Nanites
Reference to the replicators from Stargate: Atlantis