The discovery of an infant Changeling gives Odo a chance to correct what he sees as the "mistakes" in his upbringing. But as Starfleet's pressure for results grows, he has to turn to his "father," Dr. Mora
A coded message from the Gamma Quadrant leads Garak to believe his mentor, Enabran Tain, is still alive. He and Worf seek him out, only to discover something much worse: a Dominion invasion fleet poised to attack the Alpha Quadrant.
Dr. Bashir is selected to be the model for the next-generation of Emergency Medical Hologram (EMH). But he balks when his parents are invited to the station to be interviewed by the EMH programmer, Dr. Zimmerman. There is a dark secret in his family that he's afraid that his parents will reveal.
When a Cardassian official (Lawrence Pressman), who thinks of Kira (Nana Visitor) as his daughter, is dying, he agrees to reveal all he knows to her. But the experience dredges up Kira's memories of her own father's (Thomas Kopache) death.
The DS9 crew discovers a small colony on a remote world that was originally populated by them 200 years earlier due to a time-travel accident with the Defiant. The current colonists lives depend on making sure that accident happens again, even though they've now forwarned the crew that it will happen. Each crew member needs to decide if they are willing to give up their lives on DS9 in order to preserve the history of the colony.
Jake and Nog go through hell and high water, from participating in an auction to dealing with the Dominion, to receiving a Willie Mays baseball card, all in order to cheer up the war-fatigued Captain Sisko.
With the continuing battalions of Jem'Hadar entering the Alpha Quadrant in preparation for war, Sisko decides to mine the wormhole to prevent further troop movement. This provokes a confrontation between the Dominion and the Federation, forcing Sisko to abandon DS9.
Sisko and his crew crash on a barren world when their commandeered Jem'Hadar ship is shot down. They encounter Jem'Hadar who crashed there earlier, and have taken Nog and Garak hostage in exchange for medical aid for their Vorta overseer.
After forming an attack plan on the Dominion, Sisko relinquishes command of the Defiant to Dax after accepting a promotion. On DS9, the resistance faces discovery when Odo links with another changeling.
Suddenly desiring to wed within the week on DS9, Worf and Jadzia go through their own Klingon rituals: Worf on a four day bachelor party with the male members of the crew & Jadzia deals with her prospective mother-in-law, who totally opposes the idea of "an alien" marrying into her Klingon household.