In the season 6 episode "Shockwave", she is released from prison after signing Tom Card’s contract to become an official CIA asset. After Agent Pearce's reassignment to Mumbai, Agents Bailey and Manaro are requiring Fiona to fulfill the contractual obligation of her release or return to prison. Michael will not allow Fiona to do Bailey and Manaro's mission alone. After forcing Bailey and Manaro to trust in Fiona's skills, Michael provides the distraction needed to allow Fiona to finish the mission and thus manipulating Bailey and Manaro to "lose" Fiona's contract. As the team fights for a way out of Miami to save themselves, Fiona and Michael begin struggling to save their relationship. In Panama, Michael promised Fiona that when his name is clear, he is out of the agency. At the end of the season, the team is in a CIA prison. When they are released, Michael is giving orders to other agents. When Fiona confronts him, he states he did what needed to be done, but Fiona's response is he did what he wanted. She withdraws from Michael's reach in tears. He broke his promise.