Extinction

Extinction was the end of a species, caused by either the sudden death of the entire population or the slow reduction in number over a long period of time until the last members eventually died.

Mass extinctions
Major catastrophes could cause hundreds to millions of species to die out all at once. In cases of planetary destruction, all the species native to the planet could be driven to extinction (unless any native species had access to space travel).

The Last Great Time War led to the near destruction of the Daleks, as well as the destruction of many planets, star systems and even galaxies. (COMIC: Agent Provocateur) Specific planets included Eve's planet (leaving Eve the only survivor), (TV: The Mad Woman in the Attic) The Doctor was considered "the only survivor" of the Time Lords, who were thought to have been "all gone", (TV: The End of the World) but in fact, thirteen of the Doctor's incarnations had frozen Gallifrey in time and placed it in another dimension. (TV: The Day of the Doctor) The war had also resulted in all of Gallifrey's animal life going extinct, save the flies and possibly the ancient predators that they'd resurrected during the conflict. (PROSE: A Brief History of Time Lords)

By the end of the Thousand Year War between the Kaleds and the Thals, almost all animal life on Skaro was extinct. (AUDIO: Corruption) After the first generation of Daleks detonated a neutron bomb that they believed had rendered all life beyond the Dalek City extinct. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) Following the Last Great Time War, the Daleks were thought to be extinct, (TV: Dalek) before they revived their species. (TV: Victory of the Daleks) Historians would later theorise, but could not confirm, that the subsequent New Dalek Paradigm, and thus the Dalek race, would go extinct after being defeated in the Siege of Trenzalore. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) In an alternate timeline created when Rassilon allied with the Cyberiad, the Cybermen, viewing the Daleks as a threat to galactic conquest, drove their foes into extinction. The Daleks were restored when these events were undone by a remorseful Rassilon and the Twelfth Doctor. (COMIC: Prologue: The Fifth Doctor, Supremacy of the Cybermen)

In 500 million BC, the Cirranin homeworld was destroyed, leaving only Hr'oln alive. (PROSE: The Last Dodo)

In 1981, the arrival of on Logopolis fatally disrupted life there, and he killed Logopolitans at random with his Tissue Compression Eliminator. Eventually, because their Block Transfer Computations no longer worked, the planet itself began to crumble and lose coherence, as did the inhabitants. The entropy field caused by the destruction of Logopolis also destroyed a portion of the universe, including the planet of Traken. (TV: Logopolis)

At some point, the Maston's homeworld was destroyed. (AUDIO: Slipback)

During the war between the All of Us and the People, fifteen planets, three planetary rings and fifteen asteroid habitats were destroyed (PROSE: The Also People) and twenty-six billion individuals died. (PROSE: Walking to Babylon)

At the climax of the century-long war between the Thraals and the Olabrian, the Olabrians destroyed the Thraal's homeworld, wiping out all life on the planet. (PROSE: Ship of Fools)

The Veil became near-extinct when their planet's star was extinguished. The last member of the race, Androvax, went on a vengeful vendetta, destroying twelve planets before finally being arrested by the Judoon when he attempted to destroy Earth. (TV: Prisoner of the Judoon)

The Malmooth became extinct when Yana killed Chantho, the last of their species. (TV: Utopia)

The alien Stingrays travelled to San Helios and consumed all life on the planet. (TV: Planet of the Dead)

Koral became the last of her kind when her planet, Red Sky Lost, was destroyed by the Daleks. (PROSE: Prisoner of the Daleks)

All life on the planet Ceres was destroyed when a meteor collided with the planet. (TV: Sirens of Ceres)

Survivors of attacks supported by the Etydions banded together to vaporise their homeworld, cleansing it of all life. One Etydion survived, arrived on Earth and tried to convert the human race to his kind, but when he realised what he was doing, he reversed the process and died. (TV: The Custodians)

Earth mass extinctions
96% of life on Earth went extinct in around 260 million BC by the hands of the predatory Permians. (AUDIO: The Land of the Dead)

Around 65 million BC, a time travelling spaceship filled with anti-matter hit Earth, causing the destruction of the dinosaurs. (TV: Earthshock)

In the Unbound Universe, Mike Yates volunteered for a one way trip back in time and detonated forty nuclear bombs, rendering the Silurians extinct before they could awaken and threaten humanity. (AUDIO: Sympathy for the Devil)

Individual extinctions
Species would also go extinct on an individual basis, due to a variety of causes.

The Khorlthochloi went extinct in the distant past. (PROSE: Synthespians™)

A virus created from the mood drug Bliss was eventually starved to extinction when New Earth's inhabitants all died and the planet was quarantined for 100 years. (TV: Gridlock)

The Racnoss were made functionally extinct when the Tenth Doctor killed off the Racnoss Empress' children. (TV: The Runaway Bride)

Baaraddelskelliumfatrexius beasts were hunted to extinction by the Raxacoricofallapatorians. (TV: Revenge of the Slitheen)

The Arkellis flower, native to Skaro, became extinct. (PROSE: Birth of a Legend)

The Dals died out at some point before Davros was born. (AUDIO: Purity)

The Trod were destroyed by the Daleks. (COMIC: The Trodos Ambush)

By the 29th century the star whales were driven to near-extinction. Only one survived and offered help to the people remaining on a dying Earth, but it was captured and tortured by the humans, who built Starship UK around it. Three hundred years later its intent was realised and it was released by Amy Pond. It continued to serve Starship UK. (TV: The Beast Below)

The Benelisans became extinct when the Beast travelled to Benelisa and fed on them. Before they became extinct, the Benelisans sent Azoth to locate and destroy the Beast. (PROSE: The Taint)

Two hundred species, including Irradiate Grinderstag and the Stellar Raptors, were driven to extinction by the Endangered Dangerous Species Society. (PROSE: The Doctor Trap)

The Thains became extinct in 6000 BC. (PROSE: Placebo Effect)

The Tytheg became extinct by the 26th century. (PROSE: St Anthony's Fire)

The Time Lords erased the Charons before they existed as they feared that all other life in the Universe could not co-exist alongside them due to their ability to warp the fabric of the universe. Only one Charon somehow survived the death of its people and constructed a pocket universe. The Seventh Doctor confronted the Charon and learned that, after being alone for so long, it wanted to die. The Doctor sadly granted its wish. (PROSE: Sky Pirates!)

The Valnaxi were driven to near-extinction in 118 at the end of the Valnaxi-Wurm War. (PROSE: The Art of Destruction)

When the Vervoids went on a rampage on Hyperion III, the Sixth Doctor was forced to kill them all. (TV: Terror of the Vervoids)

The Aeolians were driven to near extinction in the Centaurian Catastrophe, leaving only two known survivors left. (TV: Aeolian)

The Cybershade became extinct when the CyberKing exploded. (TV: The Next Doctor)

When the Weeping Angels arrived on Alfava Metraxis, they wiped out the Aplans. (TV: The Time of Angels)

The Shugs accidentally wiped themselves out when they brought a virus from the past into their time. (PROSE: Walking to Babylon)

A tiger-like species was wiped out in unknown circumstances. Lady Huntingdon and her granddaughter Bella Huntingdon both survived and escaped to Earth. (PROSE: Old Flames)

The Fifth Doctor believed that the Jovians of Jupiter had become extinct by the 24th century. (AUDIO: The Jupiter Conjunction)

The Titanthropes became extinct before modern man appeared. (AUDIO: Last of the Titans)

The Caxtarid wiped out four indigenous sentient species on Kapteyn 5 after their conquest of the planet. (PROSE: The Room With No Doors)

The Woprat was long-extinct on Gallifrey by the time of the Doctor. (PROSE: Heart of TARDIS)

The humanoid inhabitants of an Earth-like planet became extinct, allowing the other inhabitants, the Tryods, to become the dominant species. (PROSE: The Word of Asiries)

The Deathsmiths of Goth became extinct when their Apocalypse Device killed them all. (COMIC: Black Legacy)

The Steggosians were almost completely wiped out by a plague they had caught from rats, and became extinct when the last survivor died during a conflict with the Tenth Doctor. (PROSE: The Eyeless)

Mother Nothing consumed her own race when her home planet was struck by a great famine. She died as a result of a confrontation with Captain Jack Harkness in a failed attempt to acquire the diamond engine of a space station. (AUDIO: One Enchanted Evening)

On one planet, megalovore sharks went extinct after their home, the Outland Sea boiled away during the Ice Cap Wars. (PROSE: The Secret in Vault 13)

The Hysk became extinct nine hundred years before the Doctor visited Archimedes. (PROSE: The Infinity Season)

The Sontarans ultimately became extinct by the "twilight years" of the universe. (AUDIO: The Eternal Battle)

Earth extinctions
The dodo went extinct in 1681. (PROSE: The Last Dodo)

Numerous species went extinct during the Ozone Purge of 2106, including sheep, sparrows and cats. (PROSE: Lucifer Rising)

Tigers went extinct before 2148. (PROSE: St Anthony's Fire)

Badger pirates were created when the badger became extinct. (PROSE: The Pirate Loop)

Begonias went extinct before the 24th century, but were brought back with seeds found by Bernice Summerfield. (PROSE: The Mary-Sue Extrusion)

By the 30th century, all species of wild plants and animals had become extinct except for humanity and the rat. (PROSE: Just War)

Other references
The last survivor of the Astrophia Tribe became a hunter, collecting the last members of several extinct species. (COMIC: Agent Provocateur)

The Museum of the Last Ones was a museum that preserved and kept a single living specimen of every extinct species. (PROSE: The Last Dodo)

The Silurians were capable of bringing species back from extinction, such as many species of dinosaurs. (PROSE: Blood Heat)

The Klempari defence was a common ruse in interrogation. The subject would claim to be the last of their kind. When the Eleventh Doctor questioned the Silurian, Alaya, she claimed to be the last of her species. He knew she was lying because he was the last of his species, and told her not to insult him. (TV: The Hungry Earth)

Behind the scenes
According to non-narrative information in DWBIT 41, the Aridians were exterminated by the Daleks after they destroyed the Mire Beasts.