Plot summary
S.H.I.E.L.D. keeps Daisy in containment while she is showing withdrawal symptoms after losing her connection to Hive, but her intel allows them to find the base from which Hive is attempting to launch the warhead. With Talbot's military contacts, S.H.I.E.L.D. is able to disable the rocket while a team of agents infiltrates the base, captures Hive, and extracts Radcliffe, with the latter agreeing to cooperate with S.H.I.E.L.D. and revealing that the Primitive process is irreversible.
Giyera and James steal the warhead and, while S.H.I.E.L.D. is focused on locating it, detonate a bomb they smuggled into the S.H.I.E.L.D. hangar, releasing some of Radcliffe's pathogen. Several S.H.I.E.L.D. agents transform into Primitives that free Hive from his containment and he proceeds to steal Zephyr One, S.H.I.E.L.D.'s airborne mobile command that could take the warhead high enough for the pathogen to transform a large portion of humanity. Daisy escapes and confronts Hive, begging him to connect to her again.
Credits
Adapted from Wikipedia contributors, Agents of S.H.I.E.L.D. season 3. HTML formatting and reference markers removed.