Confused Team is Confused
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When Jane Doe is taken from FBI custody by the CIA, Kurt Weller is left with more questions and regrets than answers. But he won't stop looking until he finds her, and when he does, he'll demand the truth she never had the chance to give him the night of her arrest.
Jane has weathered three hellish months at a CIA black site, enduring daily torture and interrogation by Deputy Director Jake Keaton. Her escape plan is almost ready, and when she gets out of there, she plans to hunt down Shepherd and find the answers to all of her unanswered questions. Doing it without FBI support will be difficult, but Weller burned that bridge when he threw her to the CIA. Now she's on her own.
Jane Doe/Kurt Weller, beginning just after the season one finale cliffhanger and diverging from canon.