The team deals with the revelation of Skye's altered nature, while Bobbi and Mack tell Lance where their true allegiance lie. Meanwhile, Grant and Agent 33 go on a personal mission.
To expose S.H.I.E.L.D.'s supposed crimes to the world, Cal gathers a team of "super-villains" and lures Coulson back to his hometown. Meanwhile, Melinda brings in her ex-husband to help evaluate Skye's psychological condition after her recent transformation.moreless
After a battle, Lady Sif finds herself on Earth with amnesia, and turns to S.H.I.E.L.D. for help. Meanwhile, Bobbi and Mack continue their own operation within the team, risking exposure.
While Jemma secures the Kree city, Skye is put into quarantine. Meanwhile the team carries out an operation against Hydra to eliminate the people who arranged Trip's death.
Coulson and his team prepare to destroy the Kree city, but learn where Whitehall and his people are drilling in and go to take them on. Meanwhile, Skye meets her father for the first time, and he reveals his plan to get revenge on Whitehall for killing Skye's mother.moreless
Coulson and half of the team head to San Juan to enter the Kree city, while the other half go to Vancouver to keep Raina from falling into Hydra's hands. However, Grant is one step ahead of them.moreless
While Coulson's team tries to track down the secret, they meet the Doctor. Meanwhile, Bobbi interrogates Sunil and Ward kidnaps his older brother.
Someone is killing people and leaving the alien writing etched on the corpses. As Coulson's team pursues the murderer, they discover a connection to their director's past.
Hydra impersonates S.H.I.E.L.D. and launches an attack on the UN to turn the world against Coulson and his people. As they rush to find the source of Hydra's new weapons, Coulson negotiates with the American Senator spearheaading the efforts to destroy S.H.I.E.L.D.: Grant's older brother Christian.moreless
An undercover Jemma finds herself the subject of a security crackdown by Hydra's security chief, Bobbi Morse. Meanwhile, Raina tries to negotiate with Coulson to get the obelisk before Whitehall has her killed.moreless