The full story
A cloud of Terrigen mist released into the ocean at the end of last season is quietly transforming latent Inhumans all over the world. Coulson assembles the Secret Warriors, a team of newly powered agents including Daisy Johnson, mechanic-turned-Inhuman Joey Gutierrez, and eventually Elena "Yo-Yo" Rodriguez, whose superhuman speed only lasts one heartbeat at a time. Daisy's boyfriend, S.H.I.E.L.D. psychologist Andrew Garner, is exposed to Terrigen through a booby-trapped file and transforms into Lash, a monstrous Inhuman compelled to hunt down and kill others of his own kind he judges unworthy.
Meanwhile Jemma Simmons is found alive: she spent six months trapped on a desolate world called Maveth after being pulled through the Monolith, where she met an astronaut named Will who'd been stranded there since 2001 by an earlier Hydra sacrifice. Fitz rescues Simmons through the portal and immediately starts planning to save Will too -- not knowing that Hive, an ancient parasitic Inhuman banished to Maveth centuries ago, kills Will and takes his body first.
Hydra's real founding purpose is revealed: for generations it has fed the Monolith chosen members as sacrifices meant to bring Hive home. Hydra elder Gideon Malick secretly runs the ATCU, a government Inhuman-containment agency nominally led by Rosalind Price -- who becomes a reluctant S.H.I.E.L.D. ally and a genuine partner to Coulson -- while quietly using it for unauthorized experiments. When Coulson kills Grant Ward in hand-to-hand combat, Hive simply takes over his corpse next, using Ward's memories and Malick's Hydra resources to gather followers.
With captured scientist Holden Radcliffe forced to help him, Hive develops a pathogen that turns ordinary people into primitive, mind-controlled Inhumans, intending to spread it worldwide with a stolen warhead. He also infects Daisy directly, forcing her to kill Malick and frame her new boyfriend, fellow Inhuman Lincoln Campbell, for it -- a betrayal Lash breaks by sacrificing himself to free her mind from Hive's control.
In the finale, Lincoln volunteers to fly the warhead into space to detonate it safely, throws Daisy out of the quinjet before Hive can stop him, and dies alongside Hive when it explodes -- fulfilling a vision Daisy had of an agent dying in space. Coulson, who lost his hand to Ward earlier in the season and has been fitted with an evolving prosthetic, steps down as director. Daisy, grieving Lincoln, leaves S.H.I.E.L.D. to operate alone as the vigilante Quake. Six months later, Fitz and Simmons are finally together, and Radcliffe -- traumatized by his time as Hive's captive -- has quietly uploaded an artificial intelligence he calls AIDA into an android body of her own.