1999

December

 * 30/31 December - The Doctor lands in San Francisco and is caught in a gangland shooting. As the result of exploratory heart surgery meant to save him, he regenerates into his eighth incarnation, and prevents the Master from using the Eye of Harmony to destroy Earth. (DW: Doctor Who (1996))
 * During the above period, natural phenomenon are reported in the San Francisco Bay area, including unusual tides, flood warnings. Meanwhile, snow is reported in Hawaii. Scientists link this to fluctuations in Earth's gravitational pull that occur only once every 1,000 years (though the real reason involves The Master opening the Eye of Harmony). (DW: Doctor Who (1996))
 * 31 - The Doctor and Mel crash a party hosted by the Auton Alisha Hammersmith, and defeat another invasion by the Nestene Consciousness. (DWM: Plastic Millenium)
 * 31 - To ring in the new year, the Institute for Technological Advancement & Research in San Francisco establishes San Francisco Mean Time by unveiling the world's most accurate atomic clock. The Eighth Doctor and Grace Holloway crash (and disrupt) the party in order to obtain components needed to defeat the Master. The Master causes the death of Grace Holloway and Chang Lee, but they are soon brought back to life by the Doctor. Later, just before the clock strikes midnight, Grace declines an invitation to travel with the Doctor. (DW: Doctor Who (1996))
 * 31 - The Doctor also comes and stops the bug (probably with a little help from his sixth incarnation) just as the New Year arrives. (PDA: Millennium Shock)
 * 31 - While Jack Harkness fights a "Millennium Bug", Alex Hopkins kills the rest of his Torchwood 3 team, then kills himself after Jack returns, just as the New Year arrives.(TW: Fragments)
 * As a result, Jack took over Torchwood 3.


 * Late December - The Doctor saves Earth from Saraquazel, a being from before the universe and his servant, Ashley Chapel (MA: Millennial Rites)

Behind the Scenes
References in the Doctor Who Universe tend to indicate the year 2000 of the start of the millennium, rather than 2001, the technical start of that millennium.

January

 * The Face-Eater is published.
 * Salvation by Steve Lyons is published.

February

 * The Taint is published.
 * The Wages of Sin is published.
 * The Mary-Sue Extrusion by Dave Stone published.
 * 9 - Buddy Windrush, aka Bryan Mosley, who played the prop man in The Daleks' Master Plan and a pirate in The Smugglers, dies in Shipley, England.

March

 * Demontage is published.
 * Deep Blue is published.
 * The More Short Trips anthology is published.
 * 6 - Graham Armitage, who played Barney in The Macra Terror, dies in South Africa.

April

 * Revolution Man by Paul Leonard is published.
 * Players by Terrance Dicks is published.
 * Dead Romance by Lawrence Miles is published.

May

 * Dominion is published.
 * Millennium Shock is published.
 * 27 - Donald Morley, who played Jules Renan in The Reign of Terror, dies.

June

 * Unnatural History by Jonathan Blum and Kate Orman is published.
 * Storm Harvest is published.
 * Tears of the Oracle is published.

July

 * Autumn Mist is published.
 * The Final Sanction is published.
 * The Sirens of Time, a multi-Doctor story co-starring Peter Davison, Colin Baker and Sylvester McCoy, is released on cassette tape and CD. This audio drama is the first release by Big Finish Productions under its new licence with the BBC, allowing them to produce officially sanctioned audio productions featuring concepts and cast members from Doctor Who (Big Finish had already released audio dramas featuring Bernice Summerfield.) The Big Finish line would prosper over the next decade and help fill the void left by the lack of a television series prior to 2005 and after.

August

 * The first and second volumes of Interference by Lawrence Miles are published.
 * Return to the Fractured Planet is published.

September

 * The Blue Angel co-written by Paul Magrs is published.
 * City at World's End is published

October

 * The Taking of Planet 5 is first published.
 * Divided Loyalties by Gary Russell is first published.
 * The Joy Device First Published
 * Phantasmagoria starring Peter Davison is released.


 * 1 - Noel Johnson, who played King Thous in The Underwater Menace and Charles Grover in Invasion of the Dinosaurs, dies.
 * 30 - Cavan Kendall, who played Achilles in "The Myth Makers," dies.
 * 31 - "Treehouse of Horror X", an episode of the American series The Simpsons is broadcast. The episode includes a cameo appearance by the Fourth Doctor, who is kidnapped along with other TV icons such as Xena, by the Comic Book Guy.

November

 * Frontier Worlds by Peter Anghelides is published.
 * Corpse Marker by Chris Boucher is published.
 * Whispers of Terror starring Colin Baker is released.

December

 * Twilight of the Gods is published, bringing to a close the Virgin Bernice Summerfield New Adventures series of books, which began as the Virgin New Adventures series in 1991. The publication of this book ends an era, concluding the book-publishing relationship betweenDoctor Who franchise and Virgin BOoks/W.H. Allen/Target that had begun in 1973.
 * 06 - 10th anniversary of the broadcast of the final episode of Survival, which ended Doctor Who's original 26-season run on the BBC.
 * 21 - Jack Le White, who went uncredited in The Reign of Terror and The Daleks' Master Plan, dies.
 * 25 - Peter Jeffrey, who played the pilot in The Macra Terror and Count Grendel in The Androids of Tara dies at Stratford-upon-Avon from prostate cancer.

Unknown date

 * Leonard Grahame, who played Darcy Tranton in The Daleks' Master Plan, dies.