So i've thought about this a little. We know two immutable facts Jane Doe's DNA is a match for Taylor Shaw and Jane Doe's teeth have isotopes that match someone who has lived in North Africa for years. As stated below Taylor Shaw's blood sample could have been swapped out from the original case file. Also buds of adult teeth start forming at 20 weeks, with fully formed adult teeth existing between 6 months - 24 months after birth. Which correlates to Isotope testing of Jane Doe's teeth to determine where she was raised. Teeth unlike bones don't restructure every ten years, so for the most part they retain the Isotopes from when they were formed. This places Jan Doe's one molar in North Africa from the time of conception to the time it erupted approximately 5 years old, or alternatively time the molar stopped forming somewhere between 6-24 months. It may be possible to implant a fake molar for the purpose of falling out "knocked out" at a later date, or perhaps another clue.

Here is my theory, Jane Doe's father is unknown as she was raised by a single mother who worked so hard that Taylor spent a majority of her time with another family. Perhaps her father and maybe her mother were clandestine agents of some kind. They were on opposite sides, which made it impossible for them to be together. (Mothers dedication to work and ignoring parent responsibility could be explained lack of nurture because of her previous line of work). Taylor's mother gave birth to twin girls. One went with mother and the other went with father. "bad guys" found mother and took Taylor, to use as leverage to find father, but never did. Jane Doe was raised by father, probably for a short time. Then given to an orphanage (memory of room full of kids) for her safety. Jane Doe knew she had a sister, that mother was "killed", and that father was on the run. So Jane Doe becomes a badass and gets into a pilot program into the navy seals. (The scar on the back of her neck could be faked, its easy to cause a scar and only slightly difficult to age it. Or Jane could have just been a badass as a kid and gave herself the same scar as her twin sister) Jane Doe gets on a seal team that deals with counter intelligence. The team approximately 12-24 individuals finds a group, a computer, an agency, that has workable intel but for whatever doesn't act on it. Because of classified nature of the mission and the information the only way to get the information out is to put it on her body, and give herself amnesia.

The entire seal team fakes its death because the information is that important. She is given amnesia so she can't give up her team mates, the plan, and it reduces her value as a target to zero once her tattoos have been cataloged. Once the cat is out of the bag no point in killing her it would only raise suspicion, especially if the job got botched somehow.

Jane doe sees this as the perfect chance to find the people who have her sister and find her father who has been on the run.

The bad guys watch her. Her Navy seal team mates try to protect her but if they get too close the bad guys kill them because she is the lure.

Can't wait to hear what you guys think