Apocalypse How/Class 3 B

Planetary-scale Extinction of the dominant Species on the planet, via natural causes.

Anime and Manga

 * In Rave Master

Film

 * AI has every human die in an ice age; the "survivors" are robots who evolved into a new lifeform.

Literature

 * Cthulhu will do this when the stars are right. Eldritch Abominations running rampant usually falls somewhere between here and class 5.
 * Dougal Dixon's Man After Man Handwaves the natural extinction of Homo sapiens, describing species which exist on Earth 50 million years later.
 * In The Lord of the Rings - for everything except humans (Ent, Hobbits, Orcs etc).

Live Action TV

 * An episode of the second version of The Outer Limits features an extinct humanity, but surviving androids create two new humans from preserved DNA as an Adam and Eve Plot to give us a second chance. Of course, "only one mating pair" equals You Fail Biology Forever, but still satisfying, as it subverted the series' Mandatory Twist Ending. In a different episode, several people are slingshotted forward in time to an abandoned Earth by aliens. They discover that biological warfare rendered all human females infertile. Stuck in the future, the survivors mope about how humanity's still extinct (there are only five of them)... until they find one more piece of alien technology
 * In the 2000 two part episode of The Outer Limits "Final Appeal" it's revealed that all episodes are alternate timelines and futures and that while many of them actually are tied together into semi coherence. the episode ends with a time traveler with a grudge detonating a fusion bomb taking out most of the eastern seaboard, rendering their arguing about this timeline's rejection of tech stronger than a light bulb pretty much moot.
 * The backstory of Deepwater Black is that the entire human population is wiped out by a deadly virus. The only thing they could do about was to send out a ship to be pioted by clones and stocked with DNA of a large amount of people to leave Earth and apparently come back when the virus is all gone.
 * While Life After People deliberately avoids stating how the Earth's population vanishes, the lack of corpses and the pristine condition of human structures at each episode's beginning implies that it wasn't our own doing: any Class 3a extinction achievable with present-day methods would've been a lot messier.
 * In one Babylon 5 episode, the entire Markab race is wiped out by a deadly virus confined to their species, spread from their homeworld to all their colonies. This was due to their belief that the disease only befell those who acted dishonourably, and thus all of them refused to believe they had it - making any quarantine meaningless.
 * Could actually be a Stealth Class 3a, as it's at least implied that the plague's role in taking out one of the few races with useful information on how to resist the Shadows, was not a coincidence.
 * Subverted by Doctor Who (and the only category on this page that the show doesn't really fall into): the human race is explicitly stated, on several occasions (most recently "Utopia") to outlive the universe.
 * Cassandra in "The End of the World" is stated to be the "last living human" (and she promptly dies in "New Earth", the kind-of-sequel), but it's more Fantastic Racism and a screed against plastic surgery (as Cassandra is literally skin stretched into a frame).

Tabletop Games

 * Despite the violence of the setting, some planets that die in Warhammer 40000 do so in relatively natural ways, such as being consumed by warp storms and more mundane types such as massive famine from climate change and random asteroids.

Video Games

 * The Combat of Giants: Mutant Insects games has a meteor that annihilated humanity and civilization. The game itself took place 300 years later where giant mutated insects rule the world.

Web Original

 * Resident Cloudcuckoolander Karl Pilkington of The Ricky Gervais Show thinks humanity will go this route because people will get so ugly that no one will want to have sex anymore.

Real Life

 * Extrapolating current demographic trends, humans might do this due to falling birth rates everywhere. Mind you it would take several centuries even at low rates, and demographics tend to not be reliably extrapolatable.