Plot summary
Escaping the base mostly unharmed, S.H.I.E.L.D. knows that Daisy could have killed them all and believes there is hope of freeing her from Hive. Fitz and Simmons seek out transhumanist Holden Radcliffe, who believes in the improvement of humanity through enhancement and whose studies of parasites could help with counteracting Hive's abilities. Hive turns Alisha Whitley (a duplicating Inhuman ally of S.H.I.E.L.D.) and James (after first giving him terrigen which allows him to imbue objects with fire) to his cause and takes his fledgling army to interrupt Fitz and Simmons.
Daisy warns Fitz of her vision, Hive's memories of Daniels petition Simmons to move on with her romantic life, and the others kidnap Radcliffe, taking him to a town that Hive bought with Malick's remaining fortune in order to recreate the original Kree experiments that made the first Inhumans. Talbot and the ATCU use Malick's final intel to completely dismantle Hydra's remaining infrastructure, and Fitz and Simmons finally consummate their relationship.
Credits
Adapted from Wikipedia contributors, Agents of S.H.I.E.L.D. season 3. HTML formatting and reference markers removed.