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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.
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.
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.
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.
Coulson and Melinda go undercover to obtain a painting that may hold the answers to Coulson's attacks. Meanwhile, Fitz fights his own problem to help the team when the Bus is sabotaged, while Whitehall forces Raina to bring him the obelisk.
Jemma puts her cover as a researcher for Hydra at risk to stop her new organization from acquiring Donnie Gill, a Gifted who could prove valuable to both sides. Meanwhile, Fitz confronts Grant for the first time since Grant tried to kill him.
While Coulson and his team try to stop Hydra from getting the obelisk from Creel, Talbot continues his pursuit of the fugitives. Meanwhile, Mack reaches out to Fitz, while Lance must consider his future after he loses his friends.
Coulson and his team go underground to continue the fight against Hydra. Besides dealing with the American government's attempts to capture them, the team must track down a World War II artifact of amazing power.