Set after the series finale, "What You Leave Behind", these novels differ from previous Deep Space Nine books in that they form a continuing storyline. Plot points include relations between the Federation and the Dominion following the defeat of the latter in the series finale, the rehabilitation of devastated Cardassia and its relations to Bajor, Bajor's admittance into the Federation, the mirror universe, and the renewed exploration of the Gamma Quadrant. Additionally, in the style of the television series, the books contain a large number of subplots focusing on the development of specific characters.
Following the production of The Soul Key, editor Marco Palmieri left Pocket Books, replaced by Margaret Clark, who commissioned the novel The Rough Beasts of Empire (part of the Typhon Pact crossover) set five years into the series' relative future, without covering the intervening years.
To offset the departure of characters in the series finale a number of new main and recurring characters are introduced. These include The Next Generation'sRo Laren as chief of security; an Andorian science officer named Thirishar ch'Thane (or Shar for short), through whom the reader is introduced to Andorian culture; the over 100 years old Commander Elias Vaughn, who has a background in intelligence and black ops (as featured in the TNG novel, Battle of Betazed), as the station's new Executive Officer; his daughter Prynn Tenmei as the Defiant'shelmswoman; and Taran'atar, a Jem'Hadar observer sent to live on the station by Odo. Colonel (later Captain) Kira Nerys is shown as the station's new commander.
In the years between The Soul Key and Typhon Pact - Rough Beasts of Empire the station experiences more crew changes. Shar returns to Andor in order to pay more attention to his family and years later stays on Andor following its secession from the Federation. Kira retires from Starfleet to become a vedek in Bajoran religion. Vaughn succeeds her as the commanding officer of DS9. He later transfers to a deep space exploration assignment but is severely injured during the Borg invasion of 2381. Vaughn enters a permanent coma and is taken off life support in Typhon Pact - Raise the Dawn. Also just before the Borg invasion Ezri Dax transfers to the new Federation starship USS Aventine, subsequently being promoted to Captain and commanding officer when several senior officers are killed by the Borg. Ro Laren then becomes commanding officer of DS9. Following the destruction of the original DS9 Ro becomes commanding officer of the new DS9. In addition Miles O'Brien is assigned to supervise construction of the new DS9 and stays on as chief operations officer.
Books in the series, and other books with events relevant to the relaunch, are, in order of release:
The Lives of Dax (edited by Marco Palmieri, 1999 trade paperback, 2003 mass-market paperback): A compilation of pre-finale stories involving each of the Dax hosts, framed by a conversation between Ezri Dax and Vic Fontaine. The framing narrative is set two weeks after the DS9 finale and three months prior to Avatar. The book was originally published as a standalone coda to the series, as the framing narrative contains no effect upon nor foreshadowing of the Relaunch plot; but the Relaunch canon retroactively added this book several years later, as the novels came to use some of Dax's stories here as a base for the storyline.
A Stitch in Time, by Andrew Robinson (May 2000): presented as a letter from DS9-resident Cardassian spy and tailor Elim Garak (writer Andrew Robinson's character from the series) to Dr. Julian Bashir, Garak recounts his life story, and also notes developments on Cardassia after the end of the Dominion war. This book was not originally published as part of the Relaunch; but the editor of the Relaunch considers it to have the same relevance to these books as an episode of the series, starting with a reference in Avatar (wherein Dr. Bashir reads Garak's letter). A Stitch in Time has been retroactively added to the relaunch line-up.
N-Vector, by K.W. Jeter (August 2000 - November 2000): a four-issue comic book limited series/miniseries details an adventure of the crew of DS9 and the Defiant between Benjamin Sisko's disappearance and Elias Vaughn's joining the crew. In it, the crew deals with some unusual behavior by Quark which leads to the discovery of a Romulan experiment gone awry. It introduces the character of Tiris Jast, a Bolian female, who serves as executive officer of the station and commanding officer of the Defiant until Vaughn's arrival. Jast also cameos in The Next Generation - Maximum Warp, a novel duology.
Avatar, 2 books (S.D. Perry, May 2001): As Deep Space Nine recovers from the end of the war, Jem'Hadar ships attack in an attempt to restart hostilities. The station barely survives, but then a cloaked Jem'Hadar soldier is discovered on board. Meanwhile, Kira and Ro deal with a long-lost Bajoran prophecy. The book introduces all four of DS9's new regular characters.
Section 31: Abyss, (Jeffrey Lang and David Weddle, July 2001): Dr. Bashir is sent by shadowy intelligence agency Section 31 to deal with a rogue S31 agent who has taken control of a Jem'Hadar cloning facility abandoned by the Dominion after the war, and who, like Bashir, is genetically enhanced.
Divided We Fall (John Ordover and David Mack, September–October 2001): 4-part comic book miniseries published by WildStorm Comics featuring the characters of both Star Trek: Deep Space Nine and Star Trek: The Next Generation dealing with a crisis on Trill.
Gateways, Book 4: Demons of Air and Darkness (Keith R.A. DeCandido, September 2001): Part of the cross-series Gateways sequence, this book focuses on the effort to save a group of colonists endangered by radiation, and on Quark's negotiations with the mysterious aliens who claim to control access to the gateways.
Gateways, Book 7: What Lay Beyond - "Horn and Ivory" (Keith R.A. DeCandido, 2001, reprinted October 2002): In a follow up to the previous story, Kira finds herself trapped in Bajor's distant past—and must come to accept her new role on Deep Space Nine.
Mission: Gamma: The refurbished USS Defiant embarks on a mission of exploration in the Gamma Quadrant, captained by Vaughn. Meanwhile, those left behind on DS9 deal with political upheavals on Bajor. Comprises four books:
Twilight (David R. George III, September 2002). In the GQ, Elias Vaughn and Prynn Tenmei's shuttle crashes on a mysteriously deserted planet. In the AQ, a Starfleet Admiral arrives with the news that Bajor's membership in the Federation has been accepted.
This Gray Spirit (Heather Jarman, September 2002). In the GQ, Ezri Dax and Shar clash over how to help a politically torn planet. In the AQ, Cardassia's request for peace with Bajor leads to surprising repercussions.
Cathedral (Michael A. Martin and Andy Mangels, October 2002). In the GQ, Bashir, Dax and Nog are affected by a strange space-borne artefact. In the AQ, religious upheavals threaten to disrupt the upcoming Federation signing ceremony.
Lesser Evil (Robert Simpson, November 2002). In the GQ, Vaughn discovers the wreckage of a Borg vessel, containing Prynn Tenmei's mother Ruriko. In the AQ, Kira must track down a new enemy - or rather a very old one that has unexpectedly returned.
Rising Son (S.D. Perry, January 2003): Lost for months in the Gamma Quadrant, Jake Sisko has numerous adventures which end in his discovery of long-lost Bajoran religious leader Kai Opaka.
The Left Hand of Destiny (2 books, J.G. Hertzler and Jeffrey Lang, May and June 2003): Events involving Commander Worf and Chancellor Martok (co-writer J.G. Hertzler's character from the series) upon their victorious return to the Klingon homeworld Qo'noS, based around an attempted coup against Martok. This was written after Avatar but set before it.
Unity (S.D. Perry, November 2003 hardcover, December 2004 mass-market paperback): The Defiant crew returns to find DS9 under threat by the parasites seen in the TNG episode "Conspiracy".
Worlds of Deep Space Nine: three novels about six civilizations.
Volume 1: "The Lotus Flower" (Cardassia) and "Paradigm" (Andor) (Una McCormack; Heather Jarman, May 2004): Chief O'Brien and Garak work together to thwart an unusual hostage situation at the new planetary reclamation project; Shar returns home to fulfil cultural and familial obligations.
Volume 2: "Unjoined" (Trill) and "Fragments and Omens" (Bajor) (Andy Mangels & Michael A. Martin; J. Noah Kym, February 2005): Ezri Dax and Julian Bashir face unrest and revelations on Trill; the station crew encounters new challenges as Bajor integrates into the Federation.
Volume 3: "Satisfaction Not Guaranteed" (Ferenginar) and "Olympus Descending" (The Dominion) (Keith R.A. DeCandido; David R. George III, February 2005): Quark and Ro Laren investigate accusations against Quark's brother Rom; Odo deals with a strange discovery about the Founders.
Warpath (David Mack, April 2006): The Jem'Hadar Taran'atar has brutally attacked Captain Kira and Lieutenant Ro, and Commander Vaughn must track him down. Meanwhile, in the Mirror Universe, Intendant Kira plans to take over that galaxy - and more.
Fearful Symmetry (Olivia Woods, July 2008): Contains two parallel storylines. In "Book 1," Kira recovers physically and emotionally from her injuries. She distrusts everyone, dealing with the mirror version of Iliana Ghemor, who slowly reveals our universe's Iliana's plan. "Book 2" follows Iliana's past on Cardassia, as she changes from idealistic artist to bitter widow to cold-hearted Obsidian Order agent to Bajoran imposter to abused prisoner to revenge-obsessed megalomaniac.
The Soul Key (Olivia Woods, July 2009): Continues the story of Iliana Ghemor in the Mirror Universe, as she attempts to become that universe's Emissary.
The Never Ending Sacrifice (Una McCormack, August 2009): The story of Rugal, a Cardassian boy raised by Bajorans, introduced in the episode "Cardassians".
Typhon Pact - Zero Sum Game (David Mack, November 2010): Set five years after The Soul Key. Details a covert assignment undertaken by Dr. Bashir and Sarina Douglas into Breen territory.
Typhon Pact - Rough Beasts of Empire (David R. George III, January 2011): Beginning four years after The Soul Key, this novel follows the characters of Ambassador Spock and Captain Benjamin Sisko in the aftermath of the Borg Invasion (Star Trek: Destiny) and the creation of the Typhon Pact.
Typhon Pact - Plagues of Night (David R. George III, June 2012): The cold war between the Federation and the Typhon Pact sets off a series of events leading to a climactic confrontation near Deep Space 9 and the Bajoran Wormhole.
Typhon Pact - Raise the Dawn (David R. George III, July 2012): Rogue factions within the Typhon Pact continue their goal of obtaining quantum slipstream drive, while Captains Sisko, Picard, and Ro must prevent it from happening.
The Fall - Revelations and Dust (David R. George III, September 2013): Captain Ro and her crew prepare to open the new Deep Space 9 station. Meanwhile, a rogue Typhon Pact group is suspected of setting a plot into motion that could shake the Alpha and Beta Quadrants to the core.
The Fall - A Ceremony of Losses (David Mack, October 2013): Dr. Bashir risks everything to find a cure for the Andorians' increasingly dire reproductive issues, which are slowly pushing the species toward extinction. He succeeds at the cost of a possible life sentence for treason against the Federation.