Sylvester McCoy remained the Doctor until the penultimate New Adventures, Lungbarrow, was released in March 1997. Lungbarrow, written by television author Marc Platt, was an unused storyline for the television series tying up many of the loose ends about the Doctor's origin presented as part of the "Cartmel Masterplan" and at some points flatly contradicting the Movie. The final New Adventure, The Dying Days by Lance Parkin, was the only Virgin book to feature the Paul McGann 8th Doctor. Both these books now command a pretty penny on the secondary market. They were available as PDF download on the BBC site, and thus usable in eBook readers, but are now gone. However if you search the web....
The end of the Virgin New Adventures Doctor Who line was caused by BBC deciding to bring the Doctor Who book fiction range in house at BBC books where they immediately started their own range of Eighth Doctor & Past Doctor novels. Essentially for book readers it was more of the same as many familiar authors from the Virgin ranges continued to write for the BBC.
In 1998 Big Finish Productions won a licence from the BBC to produce original Doctor Who audio plays. Peter Davison (the Fifth Doctor), Colin Baker (the Sixth Doctor) & Sylvester McCoy (the Seventh Doctor) all reprised their television roles alongside their companions, later to be joined by first Paul McGann and, recently, Tom Baker. The people behind Big Finish included both former Doctor Who magazine editor Gary Russell and Nicholas Briggs, who had previously worked on the unlicensed fan produced Audio Visuals stories - see Justyce Served - A Small Start with a Big Finish for more details.
Meanwhile the BBC itself had resurrected audio releases of missing Doctor Who stories in 1999 starting with (IIRC) The Massacre and embraced a new format for releasing stories with the DVD of the Five Doctors.
In 1999 Comic Relief decided to do a humorous Doctor Who special as part of the Red Nose Day night of programming. Producing the show was Sue Vertue, a comedy producer and the daughter of Beryl Vertue, the agent who negotiated Terry Nation's deal which retained his rights to the Daleks. Sue got her husband, Steven Moffat. the writer of acclaimed Children's show Press Gang, to write the story. Blackadder star Rowan Atkinson was cast as the Doctor with former Press Gang actress Julia Sawalha, who'd since found public recognition as Saffy in AbFab playing the companion Emma. Jonathan Pryce played the Master and actual Doctor Who series veteran Roy Skelton returned for a final outing as the Dalek Voice. The show plays on many Doctor Who tropes including, as the Doctor quickly uses up his remaining regenerations becoming, in order, Richard E. Grant, Jim Broadbent, Hugh Grant and finally Joanna Lumley, aping the much repeated rumour that the Doctor would regenerate into a woman. Yes it's humorous show, yes it's got no place with the rest of Doctor Who but somehow they hit the style and the feel dead on. The Console & Daleks for this show were sourced from fan productions and the music from older Doctor Who shows including Logopolis and The Five Doctors. I've got the VHS which also contains a decent (and humorous) making of as well as three other Doctor Who sketches from various shows and it's well worth a look.
Over the next few years new productions of Doctor Who fell into the hands of the BBC website producing in 2001 Death Comes to Time with Seventh Doctor Sylvester McCoy & companion Ace played by Sophie Aldred. The following year they produced Real Time featuring sixth Doctor Colin Baker and then the year after attempted a new adaptation of Shada starring Paul McGann and The Scream of the Shalka, featuring Richard E Grant again as well as a young David Tennant in a minor role, which was intended to be an official continuation of the series....
.... but in September of 2003, BBC 1 Controller Lorraine Heggessey announced that Doctor Who would return to television screens in 2005.