In episodes preceding this one, Gul Dukat, the Cardassian who governed Bajor under the occupation, disguised himself as a Bajoran and won the favor of the ambitious Bajoran spiritual leader Kai Winn, seducing her to the path of the Prophets' evil counterparts, the Pah-wraiths; the Cardassian leader Damar has launched a rebellion against Dominion rule; and the Changeling Founders of the Dominion have developed a mysterious illness with no known cure.
This episode advances those plot lines, as Dr. Julian Bashir discovers that DS9's security chief Odo, a rogue Changeling, has been infected with the Founders' disease; Starfleet sends DS9's Bajoran second-in-command, Kira Nerys, to assist the Cardassian resistance; and Winn turns Dukat away.
Anticipating the Cardassians' objections to being advised by a Bajoran former terrorist, Sisko has Kira given a Starfleet commission to lend her more authority.
Starfleet bureaucrats stonewall his request, claiming that the records are classified and questioning Bashir's loyalty for trying to cure a disease that primarily threatens the Federation's enemies.
As an intermediate episode in a multi-episode story arc, it received criticism for having a lot of plot setup, but not much resolution.
[5] In 2016, The Washington Post called the Dominion war story arc, of which this episode is a part, possibly the "richest narrative" of the Star Trek universe.