Jake Keaton was the Deputy Director of the CIA.
He kept captive and tortured Jane at one of the CIA's dark sites in Oregon.
Keaton informed the Wellers about the bounty that had been placed for Jane's death and urged her to leave the country until they stopped the people behind the threat. When Jane refused to stay in Colorado and put Weller and Bethany in risk for her fault, Keaton provided all the ways to take her out of the country.
Eighteen months later, Keaton had no other option but to accept to work in a joint task force with the FBI and hand Jane Doe over the Bureau to investigate the new layer of bioluminescent tattoos on her body.
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