Bubonic plague

The bubonic plague — commonly called the Black Death and clinically Yersinia pestis (COMIC: Black Death White Life) — was a devastating disease which originated in the Middle Ages. It was spread by rats and fleas due to the poor sanitation of that age. (TV: The Visitation)

13th century
The entity known as the Pied Piper fed on the fear of the plague in Hamelin in 1283 and 1284. (TV: The Day of the Clown)

14th century
According to the First Doctor, a large epidemic of bubonic plague originated in 1346 when Mongols in Janibeg Khan's army besieged Kaffa. The commander of Kaffa's defenders ordered diseased corpses to be catapulted beyond the city walls. The illness could spread to the Mongols, killing many of them. Dodo Chaplet feared the idea was possibly influenced by a similar strategy employed against the Mongols at Kiev in the 13th century, and it came to be regarded as the first instance of biological warfare. Soon, Genoese merchants travelled across the Mediterranean, spreading the plague to ports in southern Europe. It moved on to Spain, France, Germany and Britain, and then to Scandinavia and Greenland. One third of the European population died as a result of the plague. (PROSE: Bunker Soldiers)

Ashildr fell victim to the Black Death in 1348. Her immune system coped and she got better, in no small part due to having been rendered effectively immortal since the 9th century due to an implanted Mire repair kit, but her children Essie, Johann, and Rue died. (PROSE: The Triple Knife, TV: The Woman Who Lived)

15th century
In 1479, Duroc, also known as Death, appeared during a bubonic plague outbreak in Cardiff until Faith stopped it before it could claim its thirteenth victim and enter the universe permanently. (TV: Dead Man Walking)

16th century
When a colony of Saturnyn came to Venice in 1580, they claimed that there was an outbreak of plague, allowing them to isolate Venice. (TV: The Vampires of Venice)

William Shakespeare's son was a victim. It was grief over his death that brought Shakespeare to his lowest emotional ebb, allowing the Carrionites to manipulate him. (TV: The Shakespeare Code)

17th century
Barnaby's parents died from the bubonic plague prior to 1605. (GAME: The Gunpowder Plot)

In 1666, escaped Terileptil convicts created a deliberately more virulent variant on the Black Death in order to infect rats with it so as to spread it to humans. The Fifth Doctor defeated them, eliminating the storage of viruses in the Great Fire of London, which was unintentionally set whilst fighting the Terileptils. (TV: The Visitation)

Another outbreak appeared to have occurred in a village in 1669. In fact, it was an instance of Macro-viruses. (COMIC: Black Death White Life)

19th century
Memories of the plague persisted as far as the 19th century and any unexplained death was attributed to the plague or, in more bizarre cases, the legendary Plague Warriors. (PROSE: Plague of the Cybermen)

20th century
In 1933, in the Zhong Ma Fortress in occupied Manchuria, the Japanese military scientist Ishii Shiro led experimentation into biological weapons development. They infected their Chinese prisoners with bubonic plague to study its effects on the human body in order to weaponise the germs. In one case, the plague spread to the victim's lungs and evolved into the highly contagious and, without treatment, 100% fatal pneumonic plague. The research was used to kill hundreds of thousands during World War II before Japan surrendered to the United States in 1945. To prevent the Russians finding out about the research, and for their own medical purposes, the Americans did not persecute the Japanese perpetrators, and even used it themselves in the Korean War. (PROSE: Log 384)

21st century
When the Cardiff Space-Time Rift became more active after it was opened by the Rift Manipulator, at least one female victim of the Bubonic plague came through into a hospital in the 21st century. She died shortly after, in isolation, but not before her presence at the hospital caused an outbreak of the plague. (TV: End of Days)

The Hotel Historia had rooms contaminated with the Black Death. The Tenth Doctor was displeased with them. (COMIC: Hotel Historia)

Behind the scenes
One possible "game over" for the video game Don't Blink has the player being sent back in time by a Weeping Angel to the year 1348 to die of Black Death.