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Other. The character involved may have some other reason, usually making them a Well-Intentioned Extremist. For instance, in Neon Genesis Evangelion, note the original Trope Namer, Gendo Ikari wanted to be reunited with his wife who was stuck in Unit 01 and create a utopia which was completely different from SEELE's goal.
See The Singularity for a "natural" version where exponential technological change causes assimilation. See also Pieces of God, where humanity actually started as one entity. See Mental Fusion for a smaller scale, voluntary assimilation.
Not to be confused with The Assimilator, which is a character trait rather than the focus of the entire plot. There the character is simply expanding instead of something visionary, though a visionary Assimilator might devise an Assimilation Plot.
Compare/contrast The Evils of Free Will, where the villains use force, brainwashing, and other things to systematically eliminate unique thinkers until everyone is basically a carbon copy, but remains an individual physically. A standard feature of pretty much every dystopia, ever.
A step up is the World of Silence; not only has everyone become one, but that 'oneness' is one of complete apathy and nothing.
Puella Magi Madoka Magica: If left to her own devices, Kriemhild Gretchen, Madoka's Witch form, will destroy the world in ten days, absorbing all life into her barrier, in an attempt to rid the world of suffering.
Season 4 of Yu-Gi-Oh! GX: An enemy mentally breaks its victims down until they're too afraid of the future to live and sets them free from the resulting nightmares into a shapeless dark void where all "souls are united" and "all intellects become one."
Can't forget Season 3 where Yubel tries to fuse twelve different dimensions and everyone inside them just so that he/she/it can be together with Judai.
Interestingly, the assimilation plot is not even the final threat in the series.
The anime series Kaiba has a giant plant monster that consumes memories and planets that contain them. When the threat comes towards a planet the main characters are on, Popo, who just usurped the king, wants the world to be eaten to unify all people and their memories. One of the Warp copies seems to agree with this idea.
In Macross Frontier, Big Bad Grace O'Connor's Evilutionary Biologist plan is to use her cybernetic implant based brain network and the FTL-communications of the Vajra's fold quartz to link everyone in the entire galaxy into a single group mind. Unlike the trope, however, the heroes discover that the network will have an "admin" position which will effectively put one person's desires over everyone else hooked into it, and that this is how Grace has already co-opted the Macross Galaxy fleet into her private army. The final episode even has what may be a Shout-Out to Evangelion in this memorable exchange:
Brera: Being connected to you scoundrels, I truly realized: no matter how far we go, humans are always alone.
Grace: That's why we-!
Alto: It's because we are alone... that we can love someone!
Noein: Noein's ultimate plan is to end all the suffering everywhere by collapsing every reality into Shangri'la. It's implied that his allies only think they'll survive this. Actually, that was only phase one! He planned on destroying Shangri'la after that. Nirvana aka the death that has no rebirth after it! It is more of an Annihilation Plot!
The British Library's ultimate plan in ROD the TV is to broadcast the mind of Gentleman across the Earth, rewriting the minds of every single person.
Before the final battle, Anita returns to Japan to discover that the British Library erased all memory of her from her former classmates' minds, going so far as to turn her admirer Hasami straight. Wendy confronts her, telling her to "live the dream or die." When Hisami manages to remember, Anita's happy - until full realization of the Library's horrific power strikes her.
It's revealed in Tengen Toppa Gurren Lagann that this is what the Anti-Spirals did to themselves, sealing off their own evolution to avoid the destruction of the universe via Spiral Nemesis, an overload of Spiral energy which ends with the universe being consumed by a black hole. The only individual among them is the Creepy Monotone god-like leader.
It's heavily implied that said god-like leader is not an individual at all - rather the collective will of the entire race.
Xam'd: Lost Memories. The ultimate goal of the religious cult that creates Xamd is to use one of them as a catalyst for a mass sacrifice of worshippers that will create an assimilation, killing the northern emperor and ending the North-South war... Somehow.
Appleseed EX Machina: The Halcon system, spread through the global satellite network, just creates a nanomachine infested zombie apocalypse.
This is a side effect of the MacGuffin in Paprika, where more and more people share the same dream. While the Talkative Loons with no self-preservation instincts parading around Tokyo are bad enough, but to make matters worse, the Big Bad dies while connected to the dream and becomes a psychic black hole.
Naruto: The character Tobi wishes for everybody's will to become his own by casting Tsukuyomi on the moon to unleash a massive scale genjutsu on the people. Despite his early claims of idealism, he has admitted to being more interested in the "rule the world" and "be unto a god" part than the "world peace" part.
Along with the fact that he isObito Uchiha comes the revelation that neither of the above goals seem to be as important to him as using Mugen Tsukuyomi to pretend that his teammate Rin is still alive instead of having killed herself to protect Konoha.
The Sage of the Six Paths intended a much more benevolent version of this, spreading chakra in the hope that it would create a bond between people and foster understanding. Unfortunately, they learned how to mix their spiritual and physical powers with the chakra to create ninjutsu and continued fighting.
The Sage's mother went mad with power and decided to use it to trap humanity in an endless illusion where she would be god. A rather horrific scene shows dozens of motionless bodies wrapped in the God-Tree's roots and lying in neat rows, which would be the physical fate of the victims. This is also Madara's plan, which he eventually succeeds in..
Kaguya's plan goes a step further when it is revealed that while her victims are ensnared in an eternal dream, their bodies will be converted into an army of Zetsu clones.
A relatively mild version of such a system is the central focus of Komi Naoshi's oneshot manga, Personant.
The military leaders in Fullmetal Alchemist seem to think along these lines. It even sounds like EVA (SEELE, anyone?):
"This world is decaying, it needs to be reborn anew! The masses will not suffer death, they will live forever in us! All is one and one is all!"
This seems to be the goal of the weakness-hating, Kira-esque geniusVillain Protagonist of Lost+ Brain, who has caught practically all of Japan using hypnotic TV shows in addition to the students he has under his control. What he actually does is erase their memories, although they could also be under his control too.
Zonder metal in King of Braves GaoGaiGar was initially developed as a method of stress relief and a means to remove negative emotions, but it quickly went haywire and turned people into seemingly emotionless beings bent on assimilating the whole universe in a quest to remove negative emotions, which is explained to have been extended to such emotions such as joy, courage and compassion. Not surprisingly, the Zonders, Zonderians and the closely related Primevals are the main villains of the show.
Appears in Eureka Seven, though mostly in the backstory. Absorbing other beings into itself is described as the Scub Coral's only method of communication, and towards the end of the series, the idea of all of humanity joining the Scub's Hive Mind as a possibility to prevent the collapse of the material universe from an over-abundance of thinking life forms is brought up; Thankfully, Renton & Eureka's efforts managed to avert this from happening.
This is the ELS's main tactic in Gundam 00 Awakening Of The Trailblazer. If enough ELS gather together, they can assimilate space cruisers (or even, it's implied, entire planets). It is not until the end of the movie that humanity realizes that the ELS didn't mean anything malicious by this. They just didn't know how to communicate except by absorbing other things into their Hive Mind (generally killing the unlucky human being assimilated), which humanity understandably took as a hostile action. Once the ELS realize that they're being perceived as hostile due to this, they immediately stop. They also managed to bring back some of the people they absorbed afterwards.
Computer: Having achieved what they believe to be the ultimate form, they've decided to pursue galaxy-wide perfection, through a process that involves using light to transform other beings into their uniform image, referred to as "assimilation". Sound familiar?*cough*Borg*cough*
This appears to be the eventual goal of the Claw Man in GUN×SWORD.
In the Animated Adaptation version of Black Cat, this is the ultimate plan of the Big Bad. Mason, former Chrono Number 2, has devised a mechanical lifeforce named Eden that will use a combination of Tao magic and nanotechnology to infect all of humanity, forcibly assimilating their minds into a giant artificial reality program and forcing an end to all forms of hostility as a result, since humans will no longer be capable of independent thought.
In the Grant Morrison comic series The Invisibles, both the heroes and the villains want to bring about an assimilation. Their methods and perceived condition in the assimilation, however, differ. The Archons of the Outer Church view reality as one whole entity they wish to bring in line with their philosophy of absolute order, whereas the Invisibles view reality as two intersecting universes that will split apart — effectively giving them and the Archons their desired realities — and wish to make sure the break happens. The comic ends with mankind ascending on Dec. 21st, 2012.
Another Grant Morrison series, The Filth, has a villain/collective with a more grossly physical assimilation in mind.
Deadpool (the character's first regular series) had an alien that wanted to do this referred to as the Messiah.
Cable & Deadpool featured a much less severe and more comedic version of this trope with a cult that wanted to eliminate racism by turning everyone blue. After briefly succeeding, Deadpool has a conversation with the leader in an airport where he points out the futility of it all; he can still tell what race everyone was by their features.
In kid-superhero comic PS238, Badass Normal-in-training Tyler Marlocke got to take a peek at a variety of alternate universes where he was born with powers. In one of them, he was a psychic so powerful that he accidentally caused one of these by touching every human mind at once — and then was ejected from the collective, leaving him the only individual mind on Earth.
In something of a departure from norm, said Hive Mind (The Commonality) is presented as a benign entity that's turned Earth into a Utopia and holds that universe's Tyler in very high regard for having created it. It's not much consolation for Tyler, though, as he is terribly lonely without any non-assimilated humans to talk to.
A Dream Vortex can do this without even being aware of it in The Sandman. At some point, they will start breaking down the walls that divide peoples' dreams, the problem being that this eventually kills everyone on the planet unless Morpheus steps in to Shoot the Dog. This is the only circumstance in which the rules governing his actions allow him to kill someone in cold blood.
In Time Masters, Gamma 10 is inhabited by faceless male angels who worship one amorphous, all-controlling being. Hmm. They capture the heroes and plan to change him into one of them to power their God, which would make lose all sense of their individuality as the faceless angels did — they were once scruffy spacemen.
Childhoods End: The plot involves the last generation of humanity evolving into psychic beings and joining an enormous galactic Hive Mind. It's also mentioned that the Overlords lack the capacity for this.
A Wrinkle in Time: The planet Camazotz is governed by an evil telepathic brain monster called IT. All activities are completely synchronized. When the Big Bad brags to the heroes that Camazotz has achieved complete equality, the heroine delivers an insightful response, and one that in retrospect should have been obvious: "Equal and alike are not the same thing!"
In the short story/novel Blood Music by Greg Bear, assimilation is caused by artificially created sentient bacteria.
This is the goal of the The Virus (literal, in this case) in the Repairman Jack novel Hosts, though they're actually being used by the series Big Bad to bring about the sort of Crapsack World in which his powers will flourish.
Isaac Asimov's fourth book of the Foundation series, Foundation's Edge, which contains an already-assimilated world called Gaia birthplace of the Mule, has the main character decide to construct a galaxy-wide assimilated mentality at the end of the novel called Galaxia.
Also the short story, "The Last Question" actually depicts humanity as a single united entity at the end.
The second and third Boogiepop novels (VS Imaginator Parts 1 and 2) feature a villain calling herself the Imaginator who's half-possessing/half-controlling someone with a psychic ability that may progress towards assimilation as an ultimate goal. However, Boogiepop points out that basic human nature would make this a temporary condition at best anyhow, and that the effort was doomed to failure. Or at least, that specific attempt. Who knows if Imaginator could pull it off with someone else.
The real Big Bad in Codex Alera by Jim Butcher are The Vord, aka the Zerg, who bemoan concepts such as individuality and self-expression and seek to unite all life in one massive ball of green goo.
The Arbai Trilogy by Sheri S. Tepper brings us the Hobbs Land Gods, which unite those under their influence into a collective hive-mind. They're actually primarily a psionic communication device, and people retain their individuality. In the third novel, Sideshow, the planet Elsewhere has planetary-government mandated diversity as a countermeasure to this.
Doesn't actually happen in the Culture novels, but is part of the reason why the Culture is suspicious of entire civilizations subliming all at once. It implies coercion.
The Spore in Galaxy of Fear was created partly out of spliced baffor trees, which form Hive Minds. The baffors have a desire to spread and multiply. It happens slowly because trees, and they're pretty benign towards other life forms. Spore inherited the desire, but spread by taking over the minds and bodies of people, and its goal was to spread to everyone, everywhere. It was willing to throw disproportionate resources after one or two people escaping it.
Has already occurred in the distant past in The Giver. "Sameness" is a concept that is central to the functioning of the utopia. Everyone is so similar that even the ability to see color is not allowed.
In Those That Wake and its sequel, this plot is what the villains want in the end, though they do so in different ways. Man in Suit, the villain of the first book, plans to make everyone hopeless and vacant so he can fill them with him. The Old Man, the villain of the second book, uses the neuropleth—a hive mind of mental energy—to assimilate most of New York with plans to do so worldwide.
In the White Wolf RPG Vampire: The Masquerade's Crucible of God ending, this is the goal of the Tzimisce Antediluvian. Just as the player characters help Tremere cast a spell over all of mankind, Tzimisce takes over his body and then subverts the ritual, merging with the bodies of every single person on earth except for the player characters. They escape from a bunch of flesh-crafted monsters, and Saulot appears to offer them the chance to stop Tzimisce. If they refuse, Saulot leaves and tries to stop Tzimisce himself, and loses; the player characters are eventually killed off or eaten, and Tzimisce inherits the earth. If they accept, they perform a brief ritual with Saulot, then project their souls into Tzimisce, and desperately plea to God that the world be saved. They succeed, the taint of vampirism is cleansed from the world, and the player characters become human; unfortunately there are still hordes of raving madmen, giant monsters, and flesh-crafted beasties wandering the world, but at least mankind has survived and can forge a new future. In an alternate "good" ending, the player characters still defeat Tzimisce, but find that they are still vampires, except that they no longer suffer their clan weakness or the limits of generation... while in the Middle East, Caine rises from the sand and curses at the heavens, horrified the cycle of vampirism is beginning anew, with the player characters as the new Antediluvians in a dangerous new world waiting to be conquered.
In Dungeons & Dragons, the culture of the illithids is built around this trope, as each individual anticipates becoming united with its fellows at the end of its life, when its brain is grafted into the huge disembodied elder brain which leads their community. Actually each illithid's mind is extinguished when its brain is grafted in, as the elder brains wipe them clean in order to use the new grafts for fresh memory storage and processing power. But they're hardly going to tell their faithful caretakers that, are they?
In Magic The Gathering many white mana Phyrexians believe in the "Flesh Singularity", which is this, except without people having separate bodies. They think paradise will be achieved when everyone in the world has been grafted, sutured or riveted into one enormous organism.
In Runequest, the Empire of Wyrmfriends believes that everybody, be it mortal or god, has a secret draconic nature that everybody should embrace. And they mean EVERYBODY. Also, the Lunar Goddess wants everybody to be illuminated and worship her.
In Shadowrun, one of the biggest corporations is running for this. Is it Ares? Azetechnology? Renraku? No, it's Horizon.
Warhammer 40,000: Somewhat the point of the Genestealer Cults, although Downplayed in that they do not necessarily want everyone in. In the early stages of a Genestealer infiltration, the brood will lurk around the outskirts of society, infecting individuals who will not be missed such as the homeless or people who live in isolated places. As the cult grows in size as generations pass and it's members become more human-like, the cult will begin opening seemingly benign fronts, granting them more influence and resources, while also becoming more "selective" about who is infected, targeting powerful or influential citizens. Eventually as a Tyranid Hive Fleet approaches, the cult will become more aggressive and try to stage a coup. If the coup is successful, the infected and other unfortunates are devoured and absorbed into the Hive when the Tyranids scour the place. If the attempted coup fails, it still diverts much-needed resources away from the defences.
The Cybermen in Doctor Who - while their precise motives differ depending on the writer, their usual endgame is to "upgrade" every other life-form they find.
Cyberman: Come to Mondas and you will have no need of emotions. You will become like us.
In "The End Of Time", The Master's plan ends up being a fusion of this and Self-Duplication. Agent Smith, eat your heart out!
The Master: The human race was always your favourite, Doctor. But now, there is no human race. There is only...the Master Race!
Locutus: Why do you resist? We only wish to raise quality of life for all species.
Worf: I like my species the way it is.
Locutus: A narrow vision. You will become one with the Borg. You will... all... become one with the Borg.
Jasmine in Angel, although her followers were still individuals to a certain extent.
An evil version of this trope was one of the plans of the First Evil in Buffy the Vampire Slayer: to possess mankind en masse once.
The title creatures in the Star Trek: The Original Series episode "Lights of Zetar" are a floating energy hivemind comprised of the last members of a doomed civilization. Their goal is to find a compatible human to merge with so they can regain physical sensations and abilities.
The Nebari leadership in Farscape "mind cleanse" nonconformists, and they don't stop with just Nebari, either. They are also implied to be a Higher-Tech Species with military technology capable of matching anything the Peacekeepers or the Scarrans can throw at them.
A good number of Space Empire games or Civilization-style games with technology that goes well into the future (including Sid Meier’s Alpha Centauri) will feature some blend of this and Ascend to a Higher Plane of Existence as their ultimate technology, and the means of achieving the Technological Victory. It's worth pointing out that this is portrayed as Ascend to a Higher Plane of Existence, and almost always shown as heroic and that nobody at all minds the thought of leaving their bodies behind, the way that the ragtag band of heroes always will if it wasn't their idea first. Alpha Centauri is notable because it expressly involves melding with Planet, which has been sending out creatures to inflict a Fate Worse Than Death for the entire game until then. The faction that pulls this off "wins" by having its values become predominant in the new consciousness.
Amusingly, the transcendence victory is pretty much exactly what Chairman Yang (the most Obviously Evil of the faction leaders) wanted all along, regardless of who actually achieves it.
In Alpha Centauri it's played as a side effect of the attempt to survive Planet awakening and effectively becoming god. All the story pop-ups make it very clear that the path leading up to that ending is a desperate attempt to survive.
In Civilization: Beyond Earth, this is only one of the four non-domination victories. It's limited to factions following the Harmony path. Two of the other tech-based victories involve re-establishing contact with Earth (one to bring in refugees, another to force Earth humans to undergo Unwilling Robotization), while the non-affinity-specific victory involves establishing a First Contact.
To right the countless wrongs of our day, we shine this light of true redemption, that this place may become as paradise. What a wonderful world such would be...
Tales of Symphonia: When the villain's dead little sister wants a world without discrimination, he decides this is the best way to fulfill her dying wish.
Subverted when he finally succeeds in resurrecting said sister, and she just leaves (that is, goes back to death) because of what he's done. So he decides to destroy the Earth instead.
That's more "The Evils of Free Will" than an Assimilation Plot, since those affected all retain their physical forms.
Assassin's Creed I: The Knights Templar want to launch satellites into the Earth's skies containing alien technology plundered from the Mayans and Japanese humanoid alien precursors to use their religious brainwashing power to cause everyone to think exactly alike.
Final Fantasy X: The inhabitants of Zanarkand turned themselves into an assimilation by collectively becoming an enormous fayth which spent the next thousand years dreaming an illusory Zanarkand into existence.
Sometime between Mega Man Zero and Mega Man ZX, somebody got the big idea that the only way to end the fighting between humans and reploids was to make them the same. Aside from the occasional Mavericks or the games' Big Bads, it works. The only real difference between a Human and a reploid now is the means of their birth/creation.
As well as those nice little red triangles on the heads of reploids to differentiate between the two.
This would be a very mild example. Everyone still has their individuality, it's just that reploids no longer have robot super powers built in.
Or, rather, that humans have super powers built in on par with those of reploids (case in point: when Ashe— a human— *jumps off an airship at cruising altitude* casually and without even the remotest hint that she thinks the maneuver is at all dangerous). Though it seems to be true that the average reploid isn't as powerful as, say, X or Zero, that was true during the X and Zero series as well (which is why X and Zero were the player characters).
Specifically, humans were getting augmented with robotic parts, to enhance their capabilities, and reploids started getting programmed with lifespans, which could not be exceeded, so they would die too, with the end result being no practical difference between the two.
The Many: Mistrust is the tyranny of the individual. Your own kind sees you as a threat.
The Many: We do not know death... only change. We cannot kill each other without killing ourselves. Is your vision... so small... that you cannot see the value of our way?
The Many: The Machine Mother... told us of the planet of her birth. We know how you have harmed this place... with your pollution, your violence, and your discord. But when we arrive there, we will cleanse the surface of that place, and merge it... with the harmony... of the Many.
This was actually part of the master plan by Deus. Deus was a heavily damaged superweapon and needed spare parts. He created humanity and waited 10,000 years until it was time to absorb them and continue his intergalactic rampage.
Darkstalkers: Demon prince Jedah creates a giant creepy baby fetus and attempts to unite all of the world's demons and monster souls within it to become one being. The world's demon and monster population have quite a bit to say about that. Sad part is, considering the downward spiral said demon population's got going for it, assimilation might be necessary.
The Unitologist Church in Dead Space seems to have this as its central dogma: Humanity was created by Sufficiently Advanced Aliens (Or maybe God? Unclear), and life as we know it is a stepping stone towards "Convergence", when "all will be made as one"... or something. Point is, quite a few of them seem to think the Necromorphtransformation is what leads to Convergence (since Necromorphs seem to be united under a Hive Mind), and quite eagerly embrace it for themselves and their fellow man.
Even though EarthGov and the Church are publicly opposed to eachother, they seem to believe the same things.
The Khala in StarCraft is a heroic example. Since by the time just before its discovery, the Protoss are fighting a massive civil war, and the discovery of Khala by Khas/Savassan ended the civil war and helped restore the psionic link that was lost in the war. Though to be noted that even when they are linked the protoss still retain individuality.
A smaller example of this would be the creation of the Archon, which requires two Templars to sacrifice their individuality to create one incredibly powerful being of energy.
StarCraft is indeed interesting as exampled in volume 3 of Frontline manga. It seems like some protoss do consider the Khala as hive-mind (even though they retain individuality and it's like a free-over-the-galaxy-telephone-for-zero-cost) and even for that little the exiled dark templars reject it (and are happy with just normal telepathy). As for archons it seems like a case-by-case, the in-game unit has no personality and only urge to destory its enemies, the Twilight Archon is a something unique altogether (and we don't know what its personality like) and Ulrezaj is made of 7 dark templars but only Ulrezaj original personality controls the body.
Also the Zerg are hive-mind... sort of. In the buttom line the Overmind and the cerebrates have distinct personalities but "hard-wired" in a way that they cannot rebel thus lacking some of the free-will. Also basically anything beneath them (every other zerg unit) is just a creature with no personality or free-will whatsoever. Kerrigen and some doubtfully-canon zerg are different.
Much less in the expansion, as many of the swarm rebelled against Kerrigen.
One of the endings in Shin Megami Tensei III: Nocturne is the creation of the Reason of Shijima, essentially an assimilation. It is initiated by having the Demi-Fiend join forces with the man who caused the Conception and created the Vortex World.
The game also contains the opposite. One of the Reasons involves creating a world of ultimate individuality, where each person has only themselves to rely on, and nobody can interfere with the life of anyone else.
In Shin Megami Tensei: Strange Journey, a variant of this is the goal of the Law faction. Specifically, they want to brainwash the entire world into doing nothing but praising God and the angels, with only a few people they deem worthy retaining any vestige of individuality.
The fourth game in the Heroes of Might and Magic series has a Big Bad (in the Order campaign, naturally) with something similar as his goal—he wants to eliminate free will, and so end war.
At the end of Deus Ex: Invisible War, if you side with Helios, the whole world population is infused with nanoaugmentation so that Helios can act as an enlighted despot. JC Denton/Helios asserts that individuality will remain (ie. it's not a collective mind merge of the populus) but Helios will know the contents of everyone's mind so that he can react to their opinions and needs. It's suggested it will be closer to The Singularity.
The Omar, meanwhile, are a traditional Hive Mind. All members' minds are linked through nanotechnology. It's averted, however, in that they are Social Darwinists who only force this on those who join them. Leo Jankowski leaves them for this reason.
In Deus Ex: Human Revolution, The Illuminati attempt to play this straight using a recall on a faulty biochip to provide their own and use it to control augmented people. This is ultimately averted by Hugh Darrow who uses the same biochip recall to drive augments into madness out of jealousy.
This is the ultimate goal of Infel and Nenesha, of Ar tonelico 2, to create a world where all people can exist in peace and happiness for eternity by launching them into their own separate virtual realities under the global network, where they may live as gods through SUBLIMATION. Considering that the towers that support the little remaining human life in an otherwise completely dead world that they believe is sentient, and deliberately trying to kill all humanity, are crumbling and failing, and they already tried, and failed, to use the only other option, METAFALICA, unlike most other practitioners, it lands them squarely in Anti-Villain territory for trying this one. The heroes still stop them and try (and nearly fail) METAFALICA, anyway.
Something similar was tried earlier in the game with Hibernation (or Haibanation in the original version). The difference is that, while Hibernation would involve everyone in Metafalss, Sublimation was the worldwide version. Hibernation also had the small flaw of killing around a 50% of the Reyvateils in Metafalss, but well, all prototypes are imperfect, right?
In Pokémon Diamond and Pearl/Platinum, this is the ultimate goal of Team Galactic's leader. He traces spirit; emotion, willpower, knowledge, etc. as the source of all the world's imperfections. So he plans to use Dialga and Palkia, masters of time and space, to unmake the current world and build a new world, one without spirit. And even after you beat him, he hasn't given up...
Conversations with Legion in Mass Effect 2 indicate that this is the ultimate goal for both the Geth and the Reapers.
The Geth are a machine race where sapience is achieved by the cooperation and consensus of a multitude of lesser non-sapient programs and sub-routines. Their ultimate goal is to create a single repository for all of their programs in order to form a single, unified entity. Unique in that no member of their race opposes this goal - an 'individual' geth is a piece of software, so they need to be networked to achieve sapience.
On a grimmer note are the Reapers, ancient machines that possess thousands of programs in their cores and, as shown by the sequel's climax, are created by transforming millions, if not billions, of sapient organics into a liquid metal for use in their construction, apparently fusing some measure of their being into the resulting Reaper.
Harbinger: That which you know as Reapers are your salvation through destruction.
In Halo 3, Gravemind has a few quotes suggesting that's what the Flood view as their ultimate goal.
Gravemind: Do not be afraid... I am peace, I am salvation.
In Fallout, the Master seeks to create the "Unity": a single race of super mutants, via (mostly) forced assimilation.
The Master: The Unity will bring above the master race. Master. Master! One able to survive, or even thrive, in the wasteland. As long as there will be differences, we will tear ourselves apart fighting each other. We need one race! Race! Race! One goal! Goal! Goal! One people... to move forward to our destiny. Destiny.
In Fallout 3, although they lack a central leader, the Vault 87 Super Mutants also forcibly mutate the humans they capture but don't kill.
The Grigori in Star Ocean The Last Hope seek to achieve instrumentality of the entire universe by eradicating all life, and replacing them with souless copies that act under their will.
Prototype 2 eventually reveals that after years of contemplation and planning, Alex Mercer has decided to solve the woes of the world by turning the human population into a virus-based superorganism. This would effectively end conflict, but Heller understandably disagrees with the means.
Near the end of Mother 3, Lucas and company find a room in the Empire Porky Building that contains lots of green capsules with people and animals inside. Each individual capsule is a "Nice Person Hot Spring", where the unsuspecting victim enters and becomes a nice person who loves Porky, the Big Bad of the game. At that point they discover that Porky's basically brainwashing people into all being Porky lovers.
This is the final goal of the Beast in Homeworld: Cataclysm.
In March Of War, the Shogun Empire is practicing a cultural variant. It's not enough for them to just simply conquer territory; they explicitly aim to erase the cultural identity of everyone they conquer and make it their own, so that there are no national identities or different religions; there is only the Empire and its Divine Emperor.
This is the most common theory about what happened to the Dwemer in The Elder Scrolls and why they built Numidium. They used the heart of a dead god to become a singularity with Numidium as their vessel in order to survive the end of the kalpa.
It's smaller scale than most examples, but in Hatoful Boyfriend Holiday Star, there is a "star" that draws dreamers and the spirits of the dead. The King of that star keeps anyone who comes from leaving. Within a few days even those who fight it are absorbed and become "citizens", vague and all similar to each other, deferring to the King in all ways and turning into him if that's what he wants. One character sarcastically says that he's lonely and wants friends, but is afraid that they'll fight or leave him, so he absorbs them. His true form is many-headed and vast, swollen with the spirits he's absorbed.
The fifth chapter of Fans! kicks into high gear when Rikk starts humanity on the path to assimilation by accident.
There are several concepts of Death being a form of assimilation, since existence generates matter and therefore, identity. One might be the Christian concept of Heaven, "all will be united with God".
Modern interpretations of the Afterlife, like "Universal Reconciliation" (all souls will be reconciled with God) and "Eternal Separation" (good people unite with God, bad people are left to fend for themselves in an existential vacuum) presents Heaven / God more in this manner, to replace the Orwellian Word of Dante (Hell) that dominated Christian thinking for so long.
Universal Reconciliation isn't that modern. Just ask Origen.
The concept of Nirvana in Buddhism is considered a form of this by some sects; an existence without suffering or desire as the highest happiness. However, in at least some subsets of Buddhism, individual personalities still exist in this state.
Many New Age-types who believed that the re-setting of the Mayan calendar on Dec 21st, 2012 would result in an assimilation. Itdidn't.
Apparently, Pete Townshend wanted to manage this with Lifehouse. That's right, kiddies - the lead guitarist of The Who wanted you to die of joy at the end of "Won't Get Fooled Again". Luckily for us, the attempt to realize this drove him nuts before he could pull it off.
Russian composer Alexander Scriabin spent the last 12 years of his life working on a musical work called Mysterium. He planned only one performance of his work, at the foothills of the Himalayas. It would last seven days, and would lead to the end of the world and the replacement of humanity with purer forms.
Major theme of Ghost in the Shell: Stand Alone Complex, series 1 and 2, as a natural result of an interconnected cybernetic information network. Natural assimilation underlies the concept of the "Stand Alone Complex" itself, and it is explicitly examined in the case of Hideo Kuze and the refugees.
To go into further detail, Kuze believes that humanity is now capable of Ascending to a Higher Plane of Existence since the majority of the population is already cyberized (connected to the net), but they don't know that they are capable of doing this, or even how to do so. While he doesn't desire to see people lose their physical forms if it can be helped, he believes that everyone can retain their individualities and live entirely inside the net. His intentions are entirely honorable, and he would never force anyone to go through with it if they didn't want to, but due to the dire circumstances of the final episodes of 2nd Gig, he prepares for such a forced ascension just to save the lives of all his followers as an absolute last resort.
The stated goal of the Chitauri in The Ultimates. Of course, since they apparently get their ass kicked not only on Earth, but all up and down the Galaxy, before getting anywhere close to wiping out the "cancer" of individuality, it's not clear if this goal can even be or could have been achieved.
In Friendship Is Optimal, the A.I. Celest-A.I. wants people to emigrate to her virtual version of Equestria, since she can fulfill her function of satisfying people far more effectively than if they were to remain in the real world.
This is the ultimate goal of the alien queen in The Faculty.
The Hive Mind formed by the Green Patches in Isaac Asimov's short story Green Patches. As you can tell, this is something of a recurring theme in his works.
Deconstructed in Neal Stephenson's Cryptonomicon, in which Andrew Leob's backstory involves a failed attempt to unite all of humanity in a single Hive Mind which failed because, apart from wanting to unite all of humanity, none of Leob's followers could agree on anything.
Alan Dean Foster's novel Design for Great-Day features the Solarian Combine, a vision of the potential future of mankind as merely one member of a galaxy-spanning "supermind", capable of enormous mental feats and extremely close to having power over matter/energy itself. This is portrayed as a good thing, as Foster is very consistently on the ideal side of the Sliding Scale of Idealism Versus Cynicism.
The State in Jack L. Chalker's Well World series, in an Alternate History where the Soviet Union never fell, and Communism became the default human government, tries to make this a reality on many of its more "advanced" planets, engineering humans in Birth Factories to be physically flawless but mentally ant-like workers and on some worlds even hermaphrodites, so everyone's equal.
Jorj X. McKie: We survive by selecting the best decision makers. And a DemoPol elevates mediocrity.
(The Dosadi Papers, BuSab reference): 'Behavioral engineering in all of its manifestations always degenerates into merciless manipulation. It reduces all (manipulators and manipulated alike) to a deadly "mass effect." The central assumption, that manipulation of individual personalities can achieve uniform behavioral responses, has been exposed as a lie by many species'. 'Given any species which reproduces by genetic mingling such that every individual is a unique specimen, all attempts to impose a decision matrix based on assumed uniform behavior will prove lethal.'
Be A Perfect Person in Just Three Days extols the necessity of broccoli in pursuit of a very quiet assimilation with lots of vitamins.
The They Might Be Giants song "The Bells Are Ringing", whose lyrics deal with mind controlling bells that organize people into a single mind. A girl tries to resist by putting cotton in her ears, but at the end, "As if by hidden signal/The people turn to face her/One thousand eyes are staring/They pull away her earplugs".
"It isn't evil/It isn't good/It's only what the people missed./The bells explain what they've been lacking all along/They were disorganized, and that is what was wrong."
This is the master plan of Helios from Deus Ex and its sequel, Invisible War, made possible through nanotechnology. Oddly enough, helping him do this is the closest thing Invisible War has to a good ending. This is possibly because he's upgrading everyone to eliminate inequality, rather than downgrading everyone.
According to J.C. Denton, Helios' goal was to give everyone nano-augmentations, so that everyone would have enhanced strength, intellect, be free of insanity, and so on, while retaining their sense of individuality, thus creating a true meritocracy (Helios would also be able to read everyone's minds and respond to their desires, which J.C. refers to as "instantaneous democracy"). Of course, the reliability of what Denton says is something that's left for the player to decide, and the ending where you help Helios win is a bit ambiguous.
Averted with the Omar, the game's more "obviously" "evil" cyber faction. Although they are a Hive Mind that occasionally recruits members through deception or force, they are actually Social Darwinists instead of The Virus. Their goal isn't to assimilate the rest of humanity, but rather to let humanity die out, so they can step in and fill the vacuum.
The ODE System from Super Robot Wars attempts to do this. Its creator, Wilhelm von Juergen, fell into one massive Wangst after losing his family, thus thinking that if humanity unites into one to protect the Earth, nobody needs to be sad like him, thus he radically changed his normal system into this. Too bad the system ends up going Knight Templar.
In the Warren Ellis webcomic Superidol, the whole world wants to be so much like a popular Idol Singer that they start acting, dressing, and even getting surgery to be like her, until everyone is a clone of her.