The Hijacking and Retaking of Zephyr One was a mission that brought together the Secret Warriors for the first and last time, in response to the event when the HYDRA-affiliated Inhuman Giyera escaped from his Containment Module and used his powers to hijack Zephyr One, bringing the Zephyr to the Schoonebeek Oil Field along with several major S.H.I.E.L.D. agents, including director Phil Coulson.
The Secret Warriors subsequently teamed up in response to Melinda May's distress call and retook the Zephyr, capturing Gideon Malick in the process. This eventually led to HYDRA being decimated in a United States Air Force operation. However, Daisy Johnson was brainwashed by Hive during the mission, and as a result was compelled to betray S.H.I.E.L.D. shortly after Malick provided intel.
Following the Battle at the Transia Corporation Building, Hive ordered Giyera to take a HYDRA team to GT Agrochemical in order to seize their research and equipment. S.H.I.E.L.D. was alerted of the raid and flew the Zephyr One to the location in order to try to stop Giyera and his team. They arrived on site and discovered that most of the material and data had been either transferred or destroyed. Leo Fitz then alerted the agents that Giyera was coming to them. After a violent fight, Giyera was defeated and knocked unconscious by Melinda May and he was taken to the Zephyr One's Containment Module for interrogation.
Giyera ultimately regained consciousness in the Containment Module and used his power on a belt buckle to force the doors of the Module to open. Leo Fitz and Alphonso Mackenzie tried to stop him but Giyera easily escaped them and ran towards the cockpit. On his way, he met Phil Coulson, who he knocked unconscious after blocking his Prosthetic Hand. Reaching the cockpit, Giyera faced Melinda May and several other S.H.I.E.L.D. agents, but managed to avoid the fight by remotely manipulating the commands of the Zephyr One, forcing it to rapidly land in Schoonebeek Oil Field. The landing knocked out most of the passengers, except Giyera and May. May managed to contact Daisy Johnson and told her about the attack before being hit by Giyera. As a response, Lincoln Campbell convinced Johnson to gather the Secret Warriors for a rescue mission.
Daisy Johnson and Lincoln Campbell gathered the two other Secret Warriors Yo-Yo Rodriguez and Joey Gutierrez and informed them of the hijacking of the Zephyr One. The flew their Quinjet to Schoonebeek Oil Field and chuted to the place before storming the HYDRA base. They decided to split up to find their friends. Meanwhile, the S.H.I.E.L.D. agents trapped in the Oil Field retreated in a storage room of the plane, doing their best to tend to Melinda May's heavy wounds and to repel the attackers.
Rodriguez and Gutierrez took an elevator and soon met a squad of six operatives, who they defeated and tied up thanks to their powers. Elsewhere in the base, Campbell took down several other HYDRA operatives. He found the HYDRA leader Gideon Malick and captured him, while Johnson reached the base's command room and released the Zephyr One. However, she was found by Hive, who swayed her with his parasites and ordered her to go back to the Playground with her friends, planning to infiltrate the S.H.I.E.L.D. base to take them down from inside.
In the meantime, Leo Fitz and Alphonso Mackenzie managed to spread teargas, repelling Lucio and his men long enough. Lucio retreated and reached the back of the plane, where he met the Secret Warriors. Although Lucio managed to paralyze Campbell, he was stabbed by Gutierrez. Meanwhile, Johnson and Rodriguez rescued the other S.H.I.E.L.D. agents. May, who was still weakened, decided to take the team away from the Schoonebeek Oil Field by flying the Zephyr One. Hive and Giyera watched the S.H.I.E.L.D. agents escape, and Giyera lamented over the fact that they had achieved nothing. However, Hive disagreed as he had successfully infected one of the S.H.I.E.L.D. agents.
Unbeknownst to S.H.I.E.L.D., Hive had swayed Daisy Johnson while she was helping her teammates to rescue their colleagues. When Phil Coulson interrogated Gideon Malick, the HYDRA leader warned him about the fact that Hive could have infected the S.H.I.E.L.D. Inhumans. Although Coulson had locked the Secret Warriors into separate Containment Chambers, Malick's warning turned out to be grounded. Indeed, under Hive's influence, Johnson escaped from containment and managed to steal the Kree Orb and several Terrigen Crystals after killing Malick. She then left the Playground and damaged the facility so that S.H.I.E.L.D. could not follow her.
Joey Gutierrez was quite shaken by the fact that he had killed Lucio, even if he had saved Lincoln Campbell by doing so. This, combined with the suspicion raised towards the Secret Warriors when Malick was killed, prompted Gutierrez to leave S.H.I.E.L.D.