Upon returning into their time, the S.H.I.E.L.D. agents were confronted by an hostile organization led by General Hale, who had previously detained Leo Fitz while the other agents were trapped in year 2091. During the Infiltration into St. Louis Aerospace Facility, S.H.I.E.L.D. discovered that Agent Piper had struck a deal with Hale, although she had been misled to think that no harm would come to the S.H.I.E.L.D. agents. Following the battle in which Yo-Yo Rodriguez loss her arms and their encounter with Sleeper Mechs, Hale's android soldiers, aboard the Principia while they were looking for Gravitonium, S.H.I.E.L.D. suspected that Hale's motives went beyond a simple military investigation on S.H.I.E.L.D..
Indeed, S.H.I.E.L.D. was ignorant that Hale had actually revived their archenemy HYDRA. Thanks to intel provided by Piper, they decided to track down Hale and to take her into custody for interrogation.
Thanks to the intel provided by Agent Piper, the S.H.I.E.L.D. team was able to hack into Hale's phone and to locate her while she was being driven through the night. Daisy Johnson sent the coordinates to the Zephyr One where Phil Coulson led the mission. S.H.I.E.L.D. landed the cloaked Zephyr One in the middle of the road, causing Hale's car to directly drive into the plane. Then, S.H.I.E.L.D. threw an incapacitating grenade through the window. Hale passed out and was taken to an interrogation cell.
Coulson joined Hale in her cell to interrogate her. As Hale claimed that she was only trying to bring S.H.I.E.L.D to justice as they were labeled a terrorist organization, Coulson confronted her about Yo-Yo Rodriguez losing her arms during a fight with Hale's Sleeper Mechs and the explosion of the Kree Orb rigged under Hale's orders. Although Hale apologized for what had happened to Rodriguez, she dismissed Coulson's accusations, claiming that she was working to prevent the extinction of Humanity.
Coulson was surprised by Hale's answer has he considered the protection of Humanity being at the core of S.H.I.E.L.D.'s ideology. He asked Hale further to get details, but the conversation did not progress as Hale and Coulson distrusted each other. As Coulson called Hale a backseat driver, Hale revealed that she had been aware that S.H.I.E.L.D. had hacked into her phone and that the whole thing was a trick. Indeed, in the meantime, Melinda May discovered that Hale's driver was Carl Creel, who threatened to blow up the Zephyr One with an exploding belt.
Coulson joined May and Piper in the plane's docking area as a Quinjet had approached the Zephyr One. The newcomer turned out to be Anton Ivanov, who worked with Hale to prevent the extinction of Humanity and ordered the S.H.I.E.L.D. agents to release the General. Once Hale joined them, both parties had an argument about what happened during the Attack on the S.H.I.E.L.D. International Inquiry and who was responsible for it. Hale then reiterated her request to have Coulson come with her.
Although May refused to acquiesce to Hale's demands, Coulson considered accepting provided his agents would be allowed to leave unharmed. May and Coulson then had an argument as May reproached Coulson with having suicidal tendencies, but in the end she let him go with Hale, Creel and Ivanov. Coulson boarded the Quinjet and was blindfolded as he left the Zephyr One.
Phil Coulson was taken prisoner in General Hale's base in the former HYDRA Preparatory Academy. There, he learned that Hale had revived the organization HYDRA and that she wanted to have both S.H.I.E.L.D. and HYDRA work together in order to prevent the extinction of Human. Thanks to his captivity, Coulson learned more about Hale's plans and her negotiations with the Confederacy. However, he refused to collaborate with her, deeming her plans as way too dangerous for Earth itself. He also discovered that General Glenn Talbot was also prisoner in the Academy.
Quake and Melinda May, who were absolutely determined to rescue Coulson and keep him alive, decided to do anything they could to find a way to locate him. Although May was reluctant at the idea, Quake decided to request assistance from Robin Hinton, meaning they had to find her at the Retreat where she was hiding with her mother.