Apocalypse How/Class 3 A

Planetary-scale Extinction of the dominant Species on the planet, via unnatural causes (ie: someone did something).

Multiple Media

 * The planet Golgafrincham in The Hitchhiker's Guide to the Galaxy: after getting rid of those useless Telephone Sanitisers, its civilisation is wiped out by a virus contracted from a dirty telephone.

Anime and Manga

 * The ultimate goal of the Dragons of Earth in X 1999.
 * What will be the outcome in Gantz if the Giant aliens succeed in their invasion. To make a long story short,
 * It becomes an important plot point in Utawarerumono that scientists accidentally roused a malignant god in the distant past and brought about one of these.
 * In the Read or Die OVA, the villain plans to play Beethoven's lost "Death Symphony" worldwide to wipe out the human race via induced suicide.
 * The Tuffle race in Dragon Ball is wiped out by the Saiyans who become giant apes at the full moon. They work under Frieza's planet trade to do this as a career choice.
 * Also done when Buu unleashes a Beam Spam of epic proportions from the Lookout and kills every human NOT on the Lookout. He turned them into food and subsequently ate them. He did all that just because he could.
 * Super Atragon: The Big Bad is attempting this to the Earth's surface by building a giant ring that--once complete--will cook the Earth's surface with radiation bombardment. Note that this method that would've actually caused a Class 5 if it was achieved.
 * This is the Big Bad's goal in Gundam SEED. Due to his method of choice, it just might reach Class 4 or Class 5.
 * After War Gundam X came very close to this. It is established that a massive Colony Drop killed 99% of the Human race at the end of the last war. It has recovered since then, however.
 * Puella Magi Madoka Magica: It is explained in episode 10 that

Comic Books

 * Y: The Last Man is a 3.5, as every male mammal on the planet dies, save for Yorick and his pet helper monkey and two male astronauts in space. The cause has been vague, but options include an ancient curse or a biological experiment gone wrong. The comic even mentions that, 7 months after the disaster struck, the first species has gone extinct as its reproductive cycle has flown by. It should be noted that the actual short-term effects look more like a Class 1. The looming fact that this is the last generation as far as most of humanity knows barring serious reproductive breakthroughs is anything but glossed over. In addition,
 * In current Martian Manhunter continuity, this is what Malefic did to Mars, using a virus to kill all Green Martians.

Films -- Live-Action

 * I Am Legend revolves around one of these. Mankind is either dead or zombified to a man, except for Will Smith . However, the animals are doing just fine, and in fact have escaped the zoos and colonised the streets of New York. (There are lions.) The Book, however, is a 3b.
 * In the movie, dogs and rats are also affected by the virus, although it's not made clear how they're doing in the larger sense. One would assume they had a dieback/zombie rate similar to humans, at least in populated areas, but nothing's said about it one way or the other.
 * 12 Monkeys had a virus exterminate 99% of humanity and render the surface uninhabitable to them due to viral residues. No other lifeforms were affected, and the animals have reclaimed the surface.
 * The plot of the James Bond film Moonraker is that the villain wants to use a Depopulation Bomb to kill all humans on Earth and repopulate it with a select group of people under his leadership.
 * Planet of the Apes and its sequels.
 * This is essentially what happened to the planet of Miranda in Serenity as the result of a botched Alliance experiment..

Literature

 * I Have No Mouth, and I Must Scream by Harlan Ellison. A giant supercomputer has nuked the Earth and kept the remaining few humans alive in order to torture them. Things get worse.
 * Alan Weisman's The World Without Us.
 * Patrick Tilley's The Amtrak Wars are set in an America that has recovered ecologically centuries after a nuclear war. A civilization of underground cities has developed from nuclear bunkers, and they are now spreading out to wage a genocidal war against the hunter-gatherer civilization that lives in the open.
 * In Tom Clancy's novel Rainbow Six, the environmentalist extremists plan this with an engineered disease to wipe the planet clean of all humans except for their own community.
 * Margaret Atwood's Oryx and Crake.
 * In Stephen Baxter's Titan,.
 * In Eva by Peter Dickinson, just about everything is done by machines, various animal species have gone extinct, and humanity has basically gotten bored with living. So huge numbers of people just commit suicide, and the titular main character,
 * In Haunted by Chuck Palahniuk is a short story called "Obsolete." In it, humans have discovered that souls that die on Earth appear on Venus, which is heaven. However, as long as people are still alive on Earth, souls will return to them. So the governments do the only logical thing to do in a Chuck Palahniuk novel and order everyone to commit suicide or be murdered so everyone gets to go to paradise.
 * The basic backplot of Orson Scott Card's Homecoming sequence, although it takes four books before you actually find that out ...
 * The "Final War," a major thread in the Bolo series of short stories, is very aptly named: the Terran Concordiat and Melconian Empire pull a Class 3 or worse on every inhabited planet either government has. Usually from ground level, with huge tanks. The overall effect is effectively a Class 2 on a Galactic scale.
 * Mephisto, a recurring Big Bad from Michael Slade's RCMP thrillers, plays Xanatos Speed Chess with this as his objective.
 * The novel White Plague reversed the usual pattern of wiping out males, using an engineered virus to wipe out most of the females on the planet, except for those who were isolated at the start of the outbreak.
 * In Greg Egan's novel Diaspora, most humans have been voluntarily converted to software, beginning around 2065.
 * In Vernor Vinge's Marooned in Realtime, we find that anyone not in stasis vanished circa 2204. Many hypotheses are raised, without resolution by the author.
 * Signal to Noise by Eric S. Nylund ends with the world as a barren wasteland due to deceleration - the engineered part comes from  A Signal Shattered explains that
 * Margaret Atwood's "Flood" trilogy had a engineered disease that was intended to be a Class 3a - wiping out humans and replacing them with a genetically modified humanoid species, but, as of the publishing of the first two books, it seems that it will be a Class 2 bordering on high Class 1
 * Towards the end of the 54-book Animorphs series, the Andalite military thinks that the only way to stop the Yeerk invasion of Earth is to release a quantum virus that will kill all humans on the planet.
 * In Octavia Butler's Xenogenesis trilogy, the last few human survivors of a nuclear war are rescued by aliens; but, although they'll be returned to a fixed-up Earth,.
 * Geologist Dougal Dixon wrote (and illustrated) the literally science fictional "Man After Man", a really quite detailed description of the various ecosystems of Earth 50 million years from now, with the base assumption that humans go extinct some time "soon" in geological terms (i.e. within the next 100,000 years or so).
 * Spiral, the second book in Koji Suzuki's Ring trilogy ends like this.

Live-Action TV

 * In Star Trek: Voyager, the Krenim had developed a weapon to delete people from history. Any offworld colonies they would have made would be retroactively removed from history. Addendum: If these civilizations had Terraformed any uninhabitable worlds, those would become Class 5 as the habitable world would never have been made habitable in the first place (at least by the people who made them so in the original timeline). It might fit Class X-2 more, because it shows that it's able to erase inorganic objects as well (Chakotay's talk with Annorax regarding simulation of erasing a comet), but the main show of the weapon is to specifically delete races, but left the planet intact for the Krenims to get it in new timeline.
 * The documentary series The Future is Wild proposes what life on Earth might look like if humanity is no longer a factor in 5 million, 100 million, and 200 million year increments. The lack of humanity is merely a MacGuffin; nothing is mentioned about how or why humanity might go. The Discover Channel broadcast Bowdlerised it by saying mankind had simply abandoned the world, and was sending a probe every couple of eons to check on the Earth's progress.
 * An environmentalist conspiracy called "The Dawn" was alleged to be plotting to achieve this, in the short-lived TV series Strange World.
 * New Doctor Who series 1 ending: the Daleks are back, and their plan is pretty much this. The Doctor's solution to save humanity?
 * The gaseous Gelth plan to kill all humans, and inhabit their corpses.
 * In Lost,
 * According to Rich, In the Community episode "Epidemiology", a Type 3A would occur within a year and a half. However, seeing as everyone is cured by turning the thermostat down to 58 degrees, one suspects this virus might have a little trouble making it out of Colorado.

Music

 * In the Flight of the Conchords song The Humans are Dead, the robots acquired poisonous gases. And they poisoned their asses.
 * Buckethead' s album Population Override manages to portray this scenario ... without saying a word! The whole album is instrumental.

Tabletop Games

 * Known to happen in Warhammer 40,000, if rarely - the setting's instruments of devastation tend to be... not as picky as this type of apocalypse requires. Nevertheless, the Eldar, especially of Craftworld Biel-Tan, are fond of utterly excising any human/ork/anyone colonies on the Maiden Worlds and returning the planets to their pristine state, conveniently erasing any sign that the world is under Eldar protection.

Theater

 * In R.U.R., the robots turn against their masters and Kill All Humans except for one. One is too few to reproduce, but the robots don't know how to do that either. So the lone survivor creates an Adam and Eve robot couple who will repopulate the world with their descendants.

Video Games

 * The second and third endings of Drakengard fall into this sort of apocalypse. The third has a glimmer of hope that it can still be averted.
 * The fifth ending causes this in another world.
 * The main objective of the villains in Tom Clancy's Rainbow Six. A group of eco-terrorists genetically engineered a weaponized, airborne-contact delayed-incubation version of Ebola so that humanity would be extinct and Mother Nature would eventually reclaim the planet. Although the real genocide was intended to come from the vaccine - as the boss villain owned the biotech corporation that had just created a useful Ebola vaccine, the initial plague outbreak would have spurred everyone surviving on Earth to buy some. Pity they were all going to be buying more plague virus in relabeled syringes...
 * Persona 3's bad ending is strongly implied to be this -- the end of all human life on Earth, due to the collective nihilism of man.
 * Shin Megami Tensei Nocturne: It's implied the Conception,, is this.
 * Star Control 2 has several variants. First, the Dnyarri (psychic slavers) ordered the destruction of the Taalo, who were immune to psychic control; it's implied that the Taalo may have slid to another dimension or universe, though. Much later, the Androsynth poke around that area of space, and are then replaced by the Orz, who don't like to talk about it. The Ilwrath will wipe out the Pkunk if you don't intervene, and the Kohr-Ah -- former slaves of the Dnyarri -- will wipe out everyone if you don't solve the game.
 * In the original Descent: FreeSpace, the Nigh Invulnerable Shivan mothership Lucifer blasted the Vasudan homeworld of Vasuda Prime to an uninhabitable ruin, killing four billion Vasudans (and considering that Vasuda Prime was largely an extremely arid desert, there could not have been much more than four billion people there).
 * The final foe in Tales of Vesperia, while mostly apathetic towards humanity throughout the game, attempts this when things hit the fan in an attempt to preserve the planet at the cost of those who have done the most damage to it.
 * The entire plot of Fragile Dreams, where almost all humans are dead as a result of
 * Ultima 6 and 7 has the Armageddon spell, which annihilates all life in the universe except the caster and people with natural immortality. (The Xorinian wisps don't think it's very powerful since it can't affect parallel universes, and like to hand it out as a Secret Test of Character. This is also why life in Britannia suffered a drastic setback 700,000 years ago...)
 * In Wing Commander III, Class 3a is the potential fate for Locanda IV due to Kilrathi bioweapons aboard missiles fired at the planet. As per the Novelization, canonically the Victory's wing fails to intercept the bioweapons.
 * The crux of Wesker's ultimate plan in Resident Evil 5, wherein he attempts "complete global saturation" of Uroburos (as he puts it) to rid humanity of its weaker kin and leaving those who can endure it's horrifying effects to inherit the land.

Web Comics

 * Bob and George We're willing to kill everyone on the planet to stop you! This being Bob and George, people at the site of the asteroid strike survive.
 * Jack. The full story still hasn't been presented, but apparently humanity was killed in a jihad by genetically engineered furries. Although it's hinted that

Web Original

 * If SCP-1101 of the SCP Foundation breaks containment, it's possible that humanity will go extinct as every single human on the planet neglects basic bodily needs in favor of debating a particular subject, like whether or not tomatoes are a fruit or vegetable.
 * In the distant backstory of RWBY, the Gods did this to Remnant because Salem incited the people to attack them, leaving only her alive. They then abandoned Remnant, shattering the moon on their way out.  In an unusual case, though, Humanity 2.0 -- a lesser, weaker strain of humankind compared to their predecessors -- somehow appeared on the planet afterwards, repopulating it.

Western Animation

 * In the 1939 animated short Peace on Earth, a civilization of cute little animals springs up after the human race wipes themselves out in endless trench warfare. In the 1955 remake Goodwill Towards Men, naturally, it's The Bomb that did mankind in.
 * Though it wasn't his intention, Vandal Savage did this in the Justice League episode Hereafter (Part II). Being immortal, he ends up very lonely.
 * Implied in Adventure Time, considering how there are sunken cities and atom bombs littered on the ground.

Real Life

 * The Voluntary Human Extinction Movement (VHEMT) professes that humanity should render itself extinct, not by violence, but by refusing to reproduce. Advocates admit that this goal is an ideal rather than any realistic expectation for the future, but still encourage people to refrain from breeding on environmental grounds.