(written from a Production point of view)
While investigating the recent murder of an Andorian dealer, the crew of DS9 learn that Vash has returned to the station. She is apparently working with Quark and the now-deceased Andorian to sell an Orb – specifically, one of the three mythical Red Orbs of Jalbador, which it is said will destroy the world if united. Having discovered the orbs, the crew accidentally brings them together in Quark's Bar, triggering the creation of a red wormhole that destroys the station.
In evacuating the station, the USS Defiant unintentionally engages in a slingshot maneuver that sends it twenty-five years into the future, where the Federation is at war with the Bajoran Ascendancy. The Ascendancy, led by Kai Weyoun 5, worships the 'True Prophets' from the red wormhole, whom the other Prophets broke away from centuries in the past. By triggering a subspace explosion, Weyoun is able to cause the end of the universe by bringing the two wormholes together.
However, a temporal anomaly results in the crew of the Defiant being able to access Deep Space 9 in the past, both around the Day of Withdrawal – when one of the Red Orbs was first used – and when DS9 was destroyed. By subtly manipulating events, the crew are able to ensure that the events that led to them being sent into the future remain unaltered. They also arrange it so that the red wormhole is collapsed when a Klingon ship they had acquired in the future detonates inside the red wormhole, thus sparing DS9 and the Defiant and averting the timeline they witnessed.
- Star Trek: Deep Space Nine - Millennium (omnibus)
- Some story elements from the trilogy were incorporated into The Fallen.
- The trilogy contains numerous references to every Star Trek series up to Star Trek: Voyager. Jean-Luc Picard plays a supporting role in book two, as does Thomas Riker. William Riker, Geordi La Forge, Kathryn Janeway, Q, the Guardian of Forever, Hugh, and many others are mentioned. Seven of Nine and the Doctor make cameos, as does James T. Kirk (although only in a vision from the Prophets based on Sisko meeting him in "Trials and Tribble-ations").
- This series reveals why the Cardassians did not destroy Deep Space 9 when they withdrew from Bajor; the self-destruct system was actually shut down by Garak, who received a memory node containing Dukat's command codes from his future self during their attempts to avert the destruction of the universe, which he used to shut the self-destruct down before erasing his memory of that future.