William T. Riker shows up on Deep Space Nine and proceeds to charm the crew, especially Major Kira. She takes him on a tour of the station and its new ship, the Defiant. Once aboard, he pulls a phaser on her, stuns her, fakes a warp-core breach and steals the ship.
Back on the station the crew realizes it is not Will Riker but his duplicate Thomas Riker. Tom Riker had been created in a transporter accident and stranded on a planet nine years earlier and was rescued about two years previously. He is now suspected to be a member of the Maquis, and thus wanted by the Cardassians. Riker has stolen the powerful Defiant to strike a heavy blow on Cardassian forces in the name of the Maquis.
Commander Sisko is placed in a difficult position. He wants the Defiant taken back and returned to his station without having to destroy her. He eventually travels to Cardassia Prime to oversee and assist the operation led by Gul Dukat to hunt Riker down.
After doing considerable damage, the Defiant heads for the Orias system in order to destroy a secret shipbuilding facility of the Obsidian Order. Gul Dukat has a conflict with Korinas, an Obsidian Order officer, who threatens to destroy any ship that would approach the system.
Suddenly, Defiant is trapped by unknown Cardassian starships coming from the Orias system. Gul Dukat is wondering what is taking place there, because the ships are clearly not members of the regular Cardassian fleet - and the Obsidian Order is strictly forbidden from possessing military equipment of any kind.
Eventually, Sisko arranges a deal: In exchange for the Defiant's sensor logs of the Orias system, Dukat will allow the Defiant and crew to return to the Federation and Riker will be sentenced to a Cardassian labor camp rather than to death. Major Kira persuades Riker to accept the terms; she promises to get him out one day. He accepts in order to save the crew, and is taken to Cardassia.