Plot summary
The S.H.I.E.L.D. board is grateful to Coulson after Fury uses Coulson's secret helicarrier to save lives during the Battle of Sokovia. They agree to merge their factions, with Coulson remaining as director and the board acting as his oversight and advisory council. Raina has a vision of an ancient Kree weapon, designed to destroy the Inhumans —those who were altered by the Kree. Gordon takes her to search for it, finding it in the cargo hold of Gonzales' ship. S.H.I.E.L.D. discovers the intruders and uses Hydra technology to track them when they teleport away, learning the location of Afterlife.
Palamas reveals Ward's true plan when she helps him kidnap Morse. Gonzales leads a delegation to Afterlife to meet Jiaying and index the community. Raina foresees war if Jiaying meets with S.H.I.E.L.D., but it is implied that she is lying in order to seize power. When Jiaying and Gonzales meet, she delivers Cal into S.H.I.E.L.D. custody, before killing Gonzales and shooting herself to start a war with S.H.I.E.L.D. rather than let her people be indexed.
Credits
Adapted from Wikipedia contributors, Agents of S.H.I.E.L.D. season 2. HTML formatting and reference markers removed.