Premiere date: September 24, 2013
The story: Mysteriously resurrected after his death during The Avengers, Special Agent Phil Coulson assembles a small team of S.H.I.E.L.D. agents—including pilot Melinda May, black-ops agent Grant Ward, engineer Leo Fitz, and scientist Jemma Simmons—to battle Centipede, an organization that seeks to create Super Soldiers of its own. Coulson also recruits “Skye,” an orphaned hacker seeking to discover her parent’s identities, who learns the ropes as the group’s personalities grow into a team. Said trust is shattered, however, by the events of Captain America: The Winter Soldier, which reveal that several S.H.I.E.L.D. agents—including Ward—are Hydra plants, and that Coulson’s friend and fellow team leader, John Garrett, is the leader of Centipede (itself a covert Hydra cell). When Skye is shot on Garrett’s orders, Coulson saves her life with the same drug that resurrected him, learning in the process that it’s produced from the blood of an alien corpse (and that he himself was the leader of the project to harvest the serum, before having his memories wiped to maintain his sanity). Garrett—whose body is deteriorating from previous injuries—steals and uses the alien blood serum, driving himself insane in the process. He is ultimately taken down by Coulson, with help from Nick Fury and Centipede test subject Mike Peterson. Coulson is named the new director of S.H.I.E.L.D. by Fury, but soon begins exhibiting some of the same drug-based madness that afflicted Garrett before his death.
Season two: Coulson and his team begin waging war against Hydra leader Werner Reinhardt (a.k.a. Daniel Whitehall) for the Obelisk, a device originally found with the Kree alien body whose blood resuscitated Coulson. Mercenary Lance Hunter joins the team, hoping to avenge his former squadmates; meanwhile, Hunter’s ex-wife, S.H.I.E.L.D. agent Bobbi Morse, infiltrates Hydra, along with Simmons. Whitehall also works with Calvin Zabo, who’s revealed to be Skye’s father, and who tells her that her birth name is Daisy Johnson. The battle culminates in an alien city buried under San Juan, where the Obelisk opens, releasing the Terrigen Mists, which activate Johnson’s latent powers as an Inhuman but kill any normal humans who are exposed to them. Emerging from a cocoon, Johnson gains an uncontrollable ability to cause earthquakes; meanwhile, Coulson kills Whitehall.
Morse and the team’s mechanic, Mack, are revealed to be members of a faction referring to itself as “The Real S.H.I.E.L.D.” led by Robert Gonzales, which split off from the main organization during the initial Hydra attack, and which oppose Nick Fury and Coulson’s policy of extreme secrecy. The two factions wage a quiet civil war with each other, which is resolved when Coulson’s preparedness helps save the world during the events of Age Of Ultron. Meanwhile, Johnson is recruited by Jiaying, an Inhuman woman eventually revealed to be her mother, to join the secretive community of Afterlife. Jiaying is ultimately shown to be an anti-human warmonger, killing Gonzales to provoke a fight with S.H.I.E.L.D. and plotting to use the Terrigen Mists to wipe humanity off the planet. When Jiaying attempts to drain Johnson’s life force, Zabo turns on her, killing his former wife. Zabo then has his memories of his years as a villain erased, and is allowed to lead a normal life; meanwhile, Johnson is placed on a new S.H.I.E.L.D. team for “gifted” individuals, mutation-inducing crystals settle into the Earth’s atmosphere, and Simmons is pulled into a mysterious Kree artifact.