As Daniel and Sam discuss the Atlantis outpost, an incoming signal comes in with Sam's old IDC code. They receive a text message to send a MALP and it shows them "Sam" at the other end – in reality, her replicator duplicate ("RepliCarter"). RepliCarter tells them how Fifth created her and she has come in advance of the others. RepliCarter wishes to be destroyed via the disruptor and Sam agrees to meet with her twin (via television) at the Alpha site to get information. RepliCarter warns Sam that Fifth plans to conquer the galaxy and with her duplicated feelings from Sam, she doesn't want Fifth to succeed. Further, Fifth has developed an immunity to the disruptor.
RepliCarter tries to force Teal'c to destroy her but Sam intervenes. To prove herself, RepliCarter shares her memory of her going through a virtual recreation of her attacking SGC and killing Jack, and realizing she couldn't go through with it. Sam accepts RepliCarter's story and warns her the Asgard have developed large-scale versions of the disruptors. While Teal'c and Sam discuss the matter, RepliCarter secretly contacts Fifth and tells him everyone is starting to accept her story and needs more time.
The two Sams work together and realize Fifth introduced a cipher into the Replicator patterns to make them immune to the disruptor. Sam asks RepliCarter to get to it through the Replicators' subspace link but RepliCarter warns that Fifth may detect her efforts. Sam asks for the Asgard to send a satellite which Teal'c will place in orbit to protect the planet for when Fifth arrives. The Carters work against time to remodulate the disruptor as RepliCarter announces Fifth has found her and will get there in two hours.
RepliCarter secretly communicates with Fifth again, and they reveal that the whole thing is a ploy to get the information on the disruptor so they can make themselves immune to it. Jack orders them to destroy RepliCarter and evacuate the base, but Sam convinces him to give them another hour. RepliCarter finds the cipher and inputs it directly into the base computer. Teal'c deploys the satellite and returns and they adjust it as Fifth's ship arrives.
They begin the evacuation but when Sam begins to take RepliCarter to Earth, Teal'c prepares to destroy her. RepliCarter secretly convinces Fifth to approach and then activates the satellite, destroying him and his ship. RepliCarter reveals the whole thing is a ploy to destroy Fifth, gain her independence, and immunize herself and the other replicators against the disruptor. Teal'c is unable to stop her and RepliCarter links with Sam to confess everything. She stops Sam's ploy to overload the generators and blow up the base, then escapes through the Stargate. RepliCarter leaves behind an arm that dissolves into dust, and Sam resolves to study the cells and find a way to beat the Replicators.