The eleventh model of what is commonly now referred to as "skinjobs" was an effort to incorporate a means by which experiences outside of known parameters could be accessed, processed, and evaluated for further interaction. In short, Naomi is the explorer, the seeker, the quester for answers. If new data is discovered, it is Naomi who is sent to investigate, examine, and incorporate it. If a new planet is discovered, Naomi is sent to survey it. If a new emotion is discovered, it is Naomi who must analyze and experience it. Everything from elements of the physical world to the psychology and behaviors of humanity that her kind wish to emulate that they don't yet understand come under Naomi's purview.
The model designated Naomi Tamsin was inserted on Picon shortly before the start of the war, documented as an assistant professor at the University of Ketos in Biology. Her true purpose was to document the human response to the war so that her own kind could make better tactical decisions and understand the responses of the enemy better. She was inserted with full awareness of her own nature, but with self-imposed programming that would prevent her from betraying her own kind if caught and interrogated - she is unable to impart the identities of other models without initially being in their presence physically first. Until she is triggered by being in one's presence she may only acknowledge only her own identity as a skinjob, but not others.
Initially excited by the prospect of the new data she'd incorporate by being part of and witnessing the Cylon Occupation, Naomi quickly became horrified. The cruelty, the devestation, the…inhumanity of it of witnessing the execution of her own people's will and the conviction and care of the humans she stood with to hold the enemy off convinced her not long before she was killed, that she wanted to place her destiny in the hands of humanity rather than her own kind.
Because it is the purpose of the eleventh model to input new experiences on behalf of the collective, their resurrections are monitored to make sure they are not corrupted before returning fully into the fold. It is not uncommon for individual members of the elevens to be boxed for this reason. However, the war effort created something of a backlog, and it wasn't until a few days after Naomi resurrected and she had managed that her plan to defect came to the attention of one of the Ones. She was promptly captured, isolated, and imprisoned to await her seemingly inevitable fate.