While several S.H.I.E.L.D. agents were trapped at the Schoonebeek Oil Field, Daisy Johnson gathered the Secret Warriors and led them to the facility, successfully rescuing her friends. All of them returned to the Playground, with Gideon Malick, thought to be the head of HYDRA, brought in S.H.I.E.L.D. custody. However, during the battle at the Oil Field, Hive had infected Johnson and taken her into his control.
When Phil Coulson interrogated Malick, the HYDRA leader told him about Hive's infection and how Hive could have infected the Secret Warriors. Although Coulson was distrustful of Malick, he decided to lock down the Playground and put the four Secret Warriors into separate Containment Chambers while Jemma Simmons and Leo Fitz ran tests to determine whether one of them was infected.
After the confinement, the Secret Warriors more or less felt that there was something wrong with the measure. Each one of them went to a different corner of the Playground, trying to find something to do until they could leave. Meanwhile, Alphonso Mackenzie monitored them all in an attempt to detect any suspect behavior among them, without finding anything convincing. Phil Coulson and Melinda May joined him as Leo Fitz and Jemma Simmons confirmed Gideon Malick was telling the truth about Hive's capabilities of infecting Inhumans. Feeling that having the Secret Warriors scattered all over the base was too dangerous, Coulson decided to put them in quarantine. Before they could act, however, the power was shut in the Playground.
During the blackout, Daisy Johnson went to the room where Malick was interrogated and brutally killed him with her powers. She then left a grenade on his body so that it would be destroyed and no one could tell that she was Hive's spy within the Playground. The blast knocked Fitz and Simmons, who were found by Coulson. Coulson told them to get some rest somewhere safe while he gathered teams to contain the Secret Warriors. Meeting Johnson, Lincoln Campbell and Yo-Yo Rodriguez in a corridor, Coulson told them about Hive's parasitic abilities. An argument erupted and the Secret Warriors locked themselves in the common room.
While Coulson ordered his fellow agents to search for a lead in the Secret Warriors' lockers and rooms, the Secret Warriors kept arguing about who could be infected, suspecting one another without being able to solve the case. Johnson assumed that they had to find out the truth by themselves and suggested to lead them to a secret elevator, to which the other agreed. However, she actually led into a Containment Chamber where Coulson expected them. Coulson locked the room and revealed that they had found the Kree Orb in Campbell's locker. Campbell denied being infected by Hive and attacked the others before being knocked out by Johnson.
All the Secret Warriors were kept in separate Containment Chambers and tested for Hive's infection. Coulson visited Johnson in her Chamber and told her that he had to disband the Secret Warriors. Johnson later broke out of her Chamber went to see Campbell in his, telling him that they should escape to be together. However, Campbell refused as it would grow suspicion towards them and he figured out that his girlfriend was actually the one infected by Hive. Daisy tried to convince Campbell that Hive's sway was the best thing she ever felt, but Campbell rejected her as Johnson had manipulated him.
Disappointed, Johnson left the Containment Chamber and secretly reclaimed the Kree Orb as well as some Terrigen Crystals. After exiting the Playground to the plane's garage, she caused a massive earthquake, dealing severe damage to the whole escape without anyone being able to stop her.
- "Daisy's still one of us. What she did here was not of her own free will. Hive infected her; she's his hostage. We need to remember that. But this... alien creature messed with the wrong team. It thinks if it breaks our legs, we'll stop fighting, but it doesn't know how damn stubborn we are, especially when it comes to protecting our own. Hive is building an Inhuman army, but we're not gonna let that happen. So strap in, because you... might feel a little bit sick after this."
- ―Phil Coulson's speech to the crew of Zephyr One
Having lost one of their best elements to their enemy, S.H.I.E.L.D., and especially Phil Coulson who had a father-daughter-like relationship with Daisy Johnson, decided to find a way to defeat Hive once and for all and to cure all the Inhumans who had been swayed by the ancient being. Despite the damage to the Playground, Melinda May managed to fly the Zephyr One out of the base so that S.H.I.E.L.D. could be mobile and ready to act. Jemma Simmons and Leo Fitz quickly identified Dr. Holden Radcliffe as one of their best shots to have a better understanding of Hive's infection's mechanisms.
Johnson joined Hive and expressed her well-being while experiencing true bonding with another being. She handed over the Kree Orb to Hive, which he would later use to lure the Kree Reapers in an attempt to harvest their blood. Moreover, Gideon Malick's death enabled Hive to tap into the late HYDRA leader's considerable wealth, allowing him to purchase the whole city of Union City. As Hive was following his own agenda and Malick was gone, HYDRA was mostly left leaderless and vulnerable, which ultimately led to its destruction.
Due to the suspicions raised towards the Secret Warriors during the attack, Joey Gutierrez was disillusioned with S.H.I.E.L.D. and this, combined with the shock of having killed Lucio when retaking the Zephyr One, made him leave the agency.