In 2014, after being exposed and defeated by Captain America and his allies in the Battle at the Triskelion, the high command of HYDRA ordered all of their sleeper agents to purge S.H.I.E.L.D. of all loyalists or non-HYDRA agents and capture all S.H.I.E.L.D. facilities to assure their survival. Having received the message, the Lead HYDRA Agent and his subordinates began to kill or capture all crew members of the Iliad aircraft carrier who were not HYDRA assets. They seized control of the carrier, and began to convert it to one of many secret bases from which HYDRA could operate.
HYDRA attempted to take control of the aircraft carrier Iliad, and the cargo it housed. Initially, HYDRA managed early victories on many parts of the ship thanks to the element of surprise. They managed to capture many members of the ship's crew, including the ship's chief engineer Alphonso Mackenzie. HYDRA also attempted to kill the ship's commander Robert Gonzales, but they only managed to injure his leg before Gonzales managed to kill his attackers.
Bobbi Morse and Isabelle Hartley boarded the ship under orders from Nick Fury to start Protocol ASTA06 and destroy the ship, in order to prevent the ship's cargo, consisting of the Monolith, from falling into HYDRA's hands. When the Lead HYDRA Agent executed a hostage, and threatened to kill more if chief-engineer Mackenzie did not give him the ship's schematics, Morse and Hartley effortlessly killed the HYDRA guards along with the officer, and liberated the agents, using a cellphone as a distraction. Morse and Hartley encouraged the former hostages to arm themselves, and helped them in their mission to save Gonzales, and blow the ship up.
When the group found Gonzales with his leg injured, they nursed him and provided him a cane in order to walk. They tried to convince him to evacuate the ship, but he insisted on helping them destroy the ship. Morse informed the group that in order to destroy the ship, she would need to put a hard drive inside a computer in the command room. Mackenzie also informed Morse that if they destroyed the Iliad, everyone on the ship would die, including the one that inserted the hard drive. Despite that, Morse insisted that it was very vital that HYDRA did not retrieve the ship's cargo.
While the group fought their way to the command room, killing many HYDRA operatives along the way, many loyal S.H.I.E.L.D. agents on other parts of the ship began to fight back in a more organized manner, and even retook parts of the ship.
When the group arrived at the command room, Mackenzie insisted that they should not follow Fury's order, as that would mean that every loyal S.H.I.E.L.D. agent on the ship would die, making all their efforts to retake the ship meaningless. Initially, Morse and Gonzales still insisted that the risk of the cargo falling into HYDRA hands was too big, but after more convincing from Mackenzie, Morse, and eventually Gonzales, relented, with Morse destroying the hard drive.
HYDRA tried to launch an attack on the command room in order to capture it, but Gonzales' group managed to repel their attack. Eventually, HYDRA lost the battle.
After the battle, the S.H.I.E.L.D. survivors on the ship decided to rebuild S.H.I.E.L.D., with Gonzales as one of its leaders. They were joined by Anne Weaver and Tomas Calderon, along with the rest of the survivors of the Battle at the S.H.I.E.L.D. Academy.
The building of two different factions of S.H.I.E.L.D. led to the S.H.I.E.L.D. Civil War.
The Monolith remained safe aboard the Iliad until the Inhuman precognitive Raina had a vision about the Kree artifact; Jiaying, the leader of the Inhumans, had Raina and Gordon board the vessel to see if the object they feared was real.