The full story
Months after the Battle of New York, Agent Phil Coulson -- killed by Loki in The Avengers and never told how he survived -- assembles a new S.H.I.E.L.D. team aboard a retrofitted plane called the Bus: veteran specialist Melinda May, field agent Grant Ward, and scientists Leo Fitz and Jemma Simmons. Investigating a man with sudden superhuman strength, they cross paths with hacktivist Skye, who is chasing the same story through her group the Rising Tide; Coulson recruits her as a consultant instead of arresting her.
The man, day-laborer Mike Peterson, was secretly enhanced by Project Centipede, an operation harvesting Extremis-derived super-soldier technology and selling it to the highest bidder. Over the season the team keeps colliding with Centipede's operatives -- chemist Raina and businessman Ian Quinn among them -- and with a shadowy figure known only as the Clairvoyant, who seems to know S.H.I.E.L.D.'s every move before it happens. Peterson, unable to control his new strength, is rebuilt against his will into a cybernetic soldier called Deathlok.
Skye spends the season chasing her own history: she was left at an orphanage as a baby by an unnamed S.H.I.E.L.D. agent, and someone has been watching her from a distance ever since. When Quinn shoots her, the team is forced to reveal how Coulson himself survived his death -- a classified program called T.A.H.I.T.I. that revived him using a serum drawn from the corpse of an unidentified blue-skinned alien, with false memories implanted to keep him from asking how. Coulson uses the same drug to save Skye's life, and starts quietly falling apart from the same side effect it gave him: a compulsion to carve a strange, repeating symbol wherever he can.
Ward, it turns out, has been playing his part for years. Flashbacks reveal he was recruited as a teenager by fellow agent John Garrett, who exposed him to Hydra long before S.H.I.E.L.D. ever signed him. When Captain America: The Winter Soldier's revelation that Hydra has occupied S.H.I.E.L.D. from the inside reaches the team, Garrett reveals himself as both a Hydra loyalist and the Clairvoyant -- his "clairvoyance" nothing more than access to S.H.I.E.L.D.'s own files -- and Ward turns on the agency alongside him, killing loyalist Agent Victoria Hand and freeing Garrett from custody.
In the finale, Garrett and Ward raid a weapons facility to unveil an army of Deathlok soldiers, only for Garrett's own failing GH-325 dependency to unravel him into violent instability. Deathlok -- swayed when Skye protects his son -- turns on Garrett, and Coulson finishes him off with an alien weapon recovered from a mission years earlier. May defeats and captures Ward. With S.H.I.E.L.D.'s old chain of command in ruins, Nick Fury -- himself presumed dead, and very much alive -- names Coulson the agency's new director and hands him coordinates to a secret base to start rebuilding from nothing. In the last scene, Coulson is caught carving his symbol again, alone and unable to stop.