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He was created by a rogue Asgard named Loki, to replace him while the real Jack O'Neill was being studied. Unbeknownst to Loki, the Asgard put safeguards in O'Neill's DNA to prevent genetic manipulation. This resulted in the clone only maturing to the level of a teenager while retaining all of the original's memories, so that Stargate Command initially assumed he was the original Jack, who had been reverted to youth for reasons unknown. During their investigation into what had happened, the young O'Neill recalled seeing an Asgard, prompting Dr. Daniel Jackson and Teal'c to investigate similar reports of alien abductions, to try and find an explanation for his transformation.
Closer examination of his DNA revealed that the young O'Neill also suffered from genetic breakdown due to Loki's cloning methods, prompting them to call the Tok'ra for assistance; it was Jacob Carter/Selmak's examination of the young O'Neill's DNA that revealed his clone status. With this knowledge - and the information acquired from questioning previous abductees - SG-1 were able to rescue the original Jack, capture Loki and contact the Asgard. Before Thor departed with Loki, Jack asked the Asgard to help his clone, so Thor fixed the young O'Neill's genetic defects to allow him to live and age at a normal rate. The young O'Neill (being assisted financially by the Air Force) was last seen attending high school to get a second chance at childhood. The two O'Neills agreed that they wouldn't keep in touch because it would just be "weird", although the colonel told his clone to contact him in an emergency. (SG1: "Fragile Balance")
O'Neill was recruited by a former Trust operative working for the Lucian Alliance. Under the impression that he would help keep the Alliance from getting their hands on a deadly Ancient device, the clone encountered SG-1 (now under the command of Lt. Colonel Cameron Mitchell), learned the truth of what was happening, and helped them escape the trap set by two rival Alliance groups. He was given a zat'nik'tel by Teal'c and encouraged to fight for good on Earth, as he was forbidden from joining the military or the Stargate Program. A year later, he was rescued from captivity in the Middle East and brought to Atlantis to help save Colonel Sheppard. (SG1: "Off Balance", "Stargate SG-1: Behind Enemy Lines")