He introduced Faction Paradox and the Time Lords' Future War in his 1997 Eighth Doctor novel Alien Bodies. At the time, he never intended for it to become a large arc: "It was never supposed to be a big murder-mystery type of thing, with this huge question hovering over it. At the time, I was planning on revealing who the enemy was in the next book I did, but Stephen Cole stopped me doing it." The first draft of his 1999 novel Interference barely even mentioned Faction Paradox, but upon learning that Kate Orman planned to include them in Unnatural History, he felt emboldened to do more with them.
At its release, Interference was the only two-part novel ever released by BBC Books, and it garnered widespread controversy. Although fans on the Internet liked and supported Interference, extremely negative reviews like Ness Bishop's in DWM 281 made Miles feel that he had "lost [his] mandate", and on 17 August 1999 he posted his resignation from writing Doctor Who. Instead, he began working on the Faction Paradox series, and by the year 2000 BBV Productions agreed to 
However, he returned to BBC Books in 2002 with The Adventuress of Henrietta Street, which introduced the major recurring villain Sabbath. "I didn't write Adventuress because I had the desperate urge to write another book," Miles said. "I did it because I needed a job."
The first story in the Faction Paradox series, the two-part audio story The Eleven Day Empire and The Shadow Play, was released in 2001. Due to the audios' popularity, BBV Productions switched their previously anthology-style Audio Adventures in Time & Space range to exclusively focus on Faction Paradox audios. However, BBV cancelled its audio line in 2004, ending the Faction Paradox Protocols. Looking for a new publisher, Miles was impressed by the actors at Magic Bullet Productions and reached out to Alan Stevens; though the resultant True History of Faction Paradox series was designed as a stand-alone release, it featured the characters of Justine and Eliza from the Protocols audios.
Meanwhile, the first Faction Paradox book, The Book of the War, was published by Mad Norwegian Press in 2002 with Miles as both main contributor and editor. This release was followed first by Miles' novel This Town Will Never Let Us Go and then by a string of Faction Paradox novels edited by Miles and published by Mad Norwegian. When Mad Norwegian cancelled the line in 2006 and the rights passed to Random Static, Miles continued as editor, but Random Static published only one Faction Paradox novel in 2007 before the rights were passed on to Obverse Books. Miles edited Obverse's first Faction Paradox book, the 2011 anthology A Romance in Twelve Parts, before ending his involvement in the series. However, the first two Obverse-published Faction Paradox novels, Against Nature and The Brakespeare Voyage, had been edited by Miles while he was still working with the range.
In 2003, Miles wrote a Faction Paradox comic, which Mad Norwegian published through Image Comics. Due to a variety of reasons, only two issues of the comic were produced and published; however, at the same time, Mad Norwegian began working with Miles on a series of Doctor Who reference guides. In these "About Time" books, cowritten with Tat Wood, Miles presented his perspective on seasons 1 through 21 of the classic Doctor Who series. Miles would later review many episodes of the modern Doctor Who series on his blog.
Despite spending much of his writing career on the Faction Paradox series, Miles considered Doctor Who inescapable and feared that he had been "tainted for life". He would later affectionately called it part of his "native mythology".
Virgin New Adventures
BBC Eighth Doctor Adventures
- Alien Bodies
- Interference - Book One: Shock Tactic
- Interference - Book Two: The Hour of the Geek
- The Adventuress of Henrietta Street
BBC Short Trips
- The Book of the War (with Simon Bucher-Jones, Daniel O'Mahony, Ian McIntire, Mags L. Halliday, Helen Fayle, Philip Purser-Hallard, Kelly Hale, Jonathan Dennis, & Mark Clapham)
- This Town Will Never Let Us Go
The Faction Paradox Protocols
- The Eleven Day Empire
- The Shadow Play
- Sabbath Dei
- In the Year of the Cat
- A Labyrinth of Histories
The True History of Faction Paradox
- Coming to Dust
- The Ship of a Billion Years
- Body Politic
- Words from Nine Divinities
- The Judgment of Sutekh