1. Kara Thrace is a Cylon sleeper agent, similar to Boomer. The difference is that her Cylon programming never quite engaged and she remained convinced of her humanity up until her death. This explains her schizoid personality, superhuman stamina, incomparable piloting skills, and instinctive ability to hot-wire a dead Cylon Raider and fly it back home to Galactica.

2. The Cylons have shown a personal interest in Kara's "destiny", and attempted to directly intervene in her life (Simon breeding facility, Leoben kidnapping and seduction on New Caprica). These were desperate attempts by the Cylons to trigger Kara's blocked Cylon programming. They could not simply kill and resurrect her, since a sleeper agent's download-on-death mechanism is not activated until her Cylon programming is triggered.

3. Kara's death crisis was brought on by the escalating psychological strain of resisting her unconcious Cylon programming. The flight from her inner self was transformed into a literal flight into oblivion. She accepted death at the moment she broke through the myth of her own humanity and realized her true Cylon nature. With her Cylon programming finally activated, she downloaded into the nearest Cylon Resurrection Ship.

4. When Lee Adama saw Kara reappear after her death, flying in her restored Viper, he was experiencing the same type of visitation that Baltar sees when Head-Six appears to him. This explains how Kara could materialize as if by magic in an undamaged ship, talk directly to Lee without first establishing radio contact, and immediately start frakking with his head. This is standard operating procedure for dead Cylon lovers.

5. Kara Thrace is the only female Cylon model who has naturally blonde hair. The original plan was that Kara was to be known as "the blonde Cylon", but that was abandoned when her programming failed to engage. The Sixes then seized on the opportunity to become known as "the bleached-blonde Cylon". Not to be upstaged, the Threes claimed the title of "the sun-streaked Cylon". It was this ruthless competition for blonde supremacy that motivated Sharon Valeri to desert the Cylon cause and swear allegiance to the Colonial Fleet.