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Instead, however, they went on their own missions to fight the Goa'uld. It was on a mission to Juna where the duplicates of Carter, Daniel, and Teal'c were captured by Cronus. Upon learning SG-1 was not human when Daniel was executed, Cronus had them taken to his ship to be studied. Later, Carter tricked Ja'din into activating Daniel's self-destruct so she could escape. She helped the real SG-1 seal off the other levels of the ship trapping the Jaffa. However, due to the damage she took while attempting to change the control-crystals, she eventually succumbed to her wounds and died in the process as the original, flesh and blood Carter looked on. (SG1: "Double Jeopardy")
The NID, having acquired the android construction equipment from Altair, along with the readings taken of SG-1, used them to create their own duplicates of SG-1, in an attempt to create their own offworld teams that will do what needs to be done.
Although the original, Alpha team was essentially SG-1 with certain crucial information such as the address for Earth deleted from their memories, later teams were created to increasingly diverge from the original to create a team that would do the job the NID wanted, culminating in the creation of the Theta team, a team consisting of ruthless versions of SG-1 based on the Goa'uld memory implants acquired from Junior. The Theta versions of Carter, O'Neill and Teal'c were described as psychopaths interested in nothing more than their own survival whilst the Theta version of Daniel Jackson was a sociopath.
Theta Carter attempted to use a device based on the Quantum Mirror to perfect a new power source despite the potential damage the device could do to reality, but she was eventually destroyed by the android O'Neill when she failed.
The Carter of Gamma team survived the events and helped to take down the NID cell. She and Daniel, the only survivors of their team, destroyed the duplication technology, took the power source they would need and departed. Their ultimate fates are unknown but they contacted their handler Mike Talbot, aka Piper, on Perseus.(SG1: "Hydra")