During the HYDRA Uprising, S.H.I.E.L.D. suffered heavy casualties at the hands of HYDRA. Nick Fury gave Agent Bobbi Morse a secret mission to start Protocol ASTA06 aboard the aircraft carrier Iliad. During this battle on the Iliad, Morse found a team of S.H.I.E.L.D. agents, including Alphonso Mackenzie, who had been captured by HYDRA. Morse distracted them by throwing her phone at them before shooting most of them; she was assisted by Isabelle Hartley, who threw a knife at the Lead HYDRA Agent.
Together with Alphonso Mackenzie and Hartley, Morse went in search of the commander of the ship, Robert Gonzales, whom they found wounded in its conference room after he was nearly assassinated by HYDRA. After they repaired Gonzales' leg, which had been injured by an axe, Morse revealed that she had been given a secret mission by Fury to destroy the ship, ensuring that HYDRA never got their hands on the Monolith. Mackenzie protested, but it was Gonzales who gave her new orders, ordering her not to go without the assistance of him and the rest of the agents.
Upon arriving at the control room, Morse was faced with the challenge of destroying the ship, knowing that doing so would cause the deaths of not just the HYDRA agents, but also the deaths of all the innocent S.H.I.E.L.D. agents still aboard. While Mackenzie attempted to persuade her not to carry it out, Gonzales reminded her that she had an order from Fury to do it. In the end, Morse choose to fight back, and, together with Mackenzie, Gonzales and Hartley, fought back against HYDRA and retook the ship, ignoring Protocol ASTA06.