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 ship-building fascility of the Obsidian Order. Gul Dukat has a conflict with an Obsidian Order officer when she threatens to destroy any Dukat's ship that would approach the Orias.
Suddenly, Defiant is trapped by unknown Cardassian starships coming from the Orias system. Gul Dukat is wondering what takes place on Orias because the Obsidian Order obviously violates the law that it may not posess warships.
Eventually, Sisko arranges a deal: In exchange for Defiant's sensor logs of Orias system, Dukat will allow the Defiant and the crew will to return to the Federation and Riker will be sentenced to a Cardassian labor camp rather than death.
Major Kira persuades Riker to accept the terms; he promises to get Riker out one day. He accepts in order to save the crew and is taken to Cardassia.
Much of the tension created in this episode comes from the moral dilemma that Sisko has to deal with. Much of the combat is seen on a display screen, similar to the Next Generation episode "The Wounded", wherein Captain Benjamin Maxwell had to be stopped from destroying Cardassian ships and stations, which would have upset the delicate peace.