Plot summary
Malick's father died in 1970, leaving him and his brother Nathaniel to lead the "religious" side of Hydra, including periodically sending a sacrificial "traveler"—chosen at random from Hydra's inner circle—through the portal for Hive to inhabit until his return. Discovering that their father used a trick to never be chosen as the traveler, Gideon does the same and Nathaniel is chosen. In the present, Gideon tells his daughter Stephanie of his vision: he believes he saw his own death at the hands of Hive. Daisy and Lincoln track down J. T. James, an untransitioned Inhuman with knowledge of Hive who gives them an ancient Kree device.
The rest of S.H.I.E.L.D. captures Giyera, Gideon's right-hand man who is now loyal to Hive. A telekinetic Inhuman, Giyera takes control of their plane and directs it to a Hydra base with most of S.H.I.E.L.D. as his prisoners. Hive comes to the Malicks' house and reveals to Gideon that he has Nathaniel's memories. As punishment for Gideon's betrayal of Nathaniel, Hive murders Stephanie in front of him.
Credits
Adapted from Wikipedia contributors, Agents of S.H.I.E.L.D. season 3. HTML formatting and reference markers removed.