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)
 * 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)
 * 31 - The Doctor and Mel crash a party hosted by the Auton Alisha Hammerson, and defeat another invasion by the Nestene Consciousness. (DWM: Plastic Millennium)
 * 31 - To ring in the new year, the Institute for Technological Advancement and 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)
 * 31 - The Doctor also comes and stops the millennium 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 Three team, then kills himself after Jack returns, just as the New Year arrives. (TW: Fragments)
 * As a result, Jack took over Torchwood Three.


 * Late December - The Doctor saves Earth from Saraquazel, a being from after 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

 * 04 - EDA: The Face-Eater is first published.
 * PDA: Salvation is first published.

February

 * BNA: The Mary-Sue Extrusion is first published.
 * 01 - EDA: The Taint is first published. Fitz Kreiner becomes a companion.
 * PDA: The Wages of Sin is first published.
 * 09 - Buddy Windrush, aka Bryan Mosley, who played the prop man in DW: The Daleks' Master Plan and a pirate in DW: The Smugglers, dies in Shipley, England.

March

 * ST: More Short Trips anthology is first published.
 * BBV: Ghosts is first released. This entry in The Time Travellers series sees several major changes made to characters, in order to further distance them from BBC-owned properties. Sylvester McCoy's character is now called The Dominie and is given a background different from that of The Doctor, while Sophie Aldred's character is now called Alice.
 * 01 - EDA: Demontage is first published.
 * PDA: Deep Blue is first published.
 * 06 - Graham Armitage, who played Barney in DW: The Macra Terror, dies in South Africa.
 * 12 - The Curse of Fatal Death, a serialized spoof based upon Doctor Who, is broadcast as part of the BBC's Comic Relief appeal. The special stars Rowan Atkinson as the "Ninth" Doctor, Jonathan Pryce as The Master and is written by Steven Moffat -- his first televised work with the franchise. Also featured is Joanna Lumley as the first female incarnation of the Doctor ever featured in a BBC-sanctioned production (and the last until Arabella Weir in Doctor Who Unbound). The special is also webcast - the first original Doctor Who-related production to be distributed this way.

April

 * BNA: Dead Romance is first published.
 * BBV: Vital Signs, the second and last episode of The Wanderer spin-off series, is first released.
 * 05 - EDA: Revolution Man is first published.
 * 26 - PDA: Players is first published.

May

 * BBV: Only Human is first released. Last episode of The Time Travellers to feature Sophie Aldred.
 * 10 - EDA: Dominion is first published.
 * 24 - PDA: Millennium Shock is first published.
 * 27 - Donald Morley, who played Jules Renan in DW: The Reign of Terror, dies.

June

 * BNA: Tears of the Oracle is first published.
 * BBV: The Choice is first released, the first of two audio dramas in the Adventures in a Pocket Universe series starring Lalla Ward as "The Mistress" (though implied to be Romana) and John Leeson as K-9.
 * 07 - EDA: Unnatural History is first published.
 * PDA: Storm Harvest is first published.

July

 * BFA: 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 would continue even after the series returned. In 2001, Big Finish will score a coup by launching a long-running series of productions featuring then-current Eighth Doctor, Paul McGann.
 * 05 - EDA: Autumn Mist is first published.
 * PDA: The Final Sanction is first published.

August

 * BNA: Return to the Fractured Planet is first published.
 * REF: The Doctor's Affect, a memoir by onetime K-9 assistant operator Stephen Cambden, first published.
 * BBC Audio, after a six-year hiatus, resumes reissuing audio recordings of Doctor Who stories that no longer exist in complete visual form in the BBC Archives. Previously, these recordings were issued exclusively on twin cassette, but they're now also being released on CD. Released this month: DW: The Massacre of St. Bartholomew's Eve, which is released under the shorter title, The Massacre.
 * 02 - EDA: Interference - Book One and Interference - Book Two are both first published, the first and only two-volume BBC Books story. Introduction of new companion Compassion. The Third Doctor also appears. Due to both EDA books coming out at once, there is no Past Doctors Adventure this month.

September

 * BBV: The Search, the second and last episode of Adventures in a Pocket Universe, is first released.
 * 06 - EDA: The Blue Angel is first published.
 * PDA: City at World's End is first published.

October

 * BNA: The Joy Device is first published.
 * BFA: Phantasmagoria is released. First solo Fifth Doctor audio adventure.
 * REF: The Nine Lives of Doctor Who is first published.
 * The first edition of REF: I, Who, a long-running guide to Doctor Who fiction, is published.
 * 1 - Noel Johnson, who played King Thous in DW: The Underwater Menace and Charles Grover in DW: Invasion of the Dinosaurs, dies.
 * 04 - EDA: The Taking of Planet 5 is first published.
 * PDA: Divided Loyalties is first published.
 * 17 - 20th anniversary of Doctor Who Magazine.
 * 30 - Cavan Kendall, who played Achilles in DW: 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

 * BFA: Whispers of Terror is released. First solo Sixth Doctor audio adventure. Nicola Bryant begins a prolific stint with Big Finish Productions, voicing many audios as Peri Brown for both the Fifth and Sixth Doctors.
 * REF: A Critical History of Doctor Who on Television by noted literary critic John Kenneth Muir, is first published.
 * 01 - PDA: Corpse Marker is first published.
 * 28 - EDA: Frontier Worlds is first published.

December

 * BNA: Twilight of the Gods is first 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 between the Doctor Who franchise and Virgin Books/W.H. Allen/Target that had begun in 1973.
 * CP: Perfect Timing 2, a Doctor Who short story collection for charity, first published.
 * 06 - 10th anniversary of the broadcast of the final episode of DW: Survival, which ended Doctor Who's original 26-season run on the BBC.
 * 21 - Jack Le White, who went uncredited in DW: The Reign of Terror and DW: The Daleks' Master Plan, dies.
 * 25 - Peter Jeffrey, who played the pilot in DW: The Macra Terror and Count Grendel in DW: The Androids of Tara dies at Stratford-upon-Avon from prostate cancer.

Unknown date

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