Award-winning science fiction writer Alastair Reynolds is to delve into the past of Doctor Who in a new novel that sees the Time Lord in his Jon Pertwee incarnation taking on the Master.

Author of the Revelation Space series and winner of British Science Fiction award for best novel, Reynolds's Harvest of Time will feature the third Doctor, as played by Pertwee, and will be published by BBC Books in 2013. A scientist for the European Space Agency before he devoted himself to writing full time, Reynolds said it "seemed natural to 'do' Pertwee [because] I've always been attracted to Pertwee's portrayal of the Doctor as dashing man-of-science, charming, sceptical and rational".

With the universe under threat from arch-nemesis and renegade Time Lord the Master – "simply my favourite fictional villain in any medium," said Reynolds – Doctor Who will be facing "the ultimate moral crisis" in Reynolds's venture into his past, according to BBC Books, battling his enemy on 20th-century Earth and far into the future.

Harvest of Time will be the first new adventure for a past doctor published since the show returned to television screens in 2005. It follows Doctor Who novels from Michael Moorcock, Naomi Alderman and Stephen Baxter, with a novelisation of Douglas Adams's "lost" Doctor Who script Shada out next year.

"I've never had much interest in spinoffery - the idea of writing in someone else's universe generally leaves me cold - but Doctor Who is different," said Reynolds. "I've grown up with it. It's been part of my life since I was tiny, watching Jon Pertwee on a grainy black and white television in Cornwall, and being terrified out of my mind. All of the usual cliches apply – I was the boy behind the settee, too afraid to look at the screen, but somehow unable to leave the room. Daleks scared the hell out of me, to the point where I wouldn't go round to another boy's house because he had Dalek wallpaper in his bedroom. Above all else, Doctor Who still seems to me to offer near-infinite scope for the writer. It must be the least constraining of televisual properties."

One of Reynolds's fans asked how the author, a scientist with a PhD in astronomy known for his hard science fiction writing, would deal with the Pertwee era's "not exactly rigorous science", including the well known phrase "reverse the polarity of the neutron flow". Reynolds said his contribution to the Who collection "won't be hard SF by any stretch", but he does "want to emphasise the Doctor as a man of science (which I think was done very effectively during the Pertwee era, even though the science itself was often daft)".