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Coulson leads an assault on the captured helicarrier, taking Cal along with them. Meanwhile, Jiaying prepares to unleash the Terrigen crystals on the world, and Skye is forced to confront her mother.
Coulson realizes that Jiaying intends to set off a war, but tries to avoid launching a counter attack for fear of hurting Skye. Meanwhile, Skye appeals to Jiaying to reconsider, and Grant tries to give Kara closure.
Tensions rise between S.H.I.E.L.D. and the Inhumans, with Skye caught in the middle. Meanwhile, Coulson reveals what he's been doing with the missing millions.
Coulson and Gonzales are forced to join forces with an unreliable ally to defeat Hydra.
Coulson and Lance turn to Grant for help. Meanwhile, Skye and Lincoln become involved in the inter-S.H.I.E.L.D. struggles.
While Skye questions her future with the Inhumans, Melinda must decide her future in the war between the two sides of S.H.I.E.L.D.
While Skye meets a fellow "Inhuman," Coulson takes on Gonzales for the future of S.H.I.E.L.D.
Skye must make a decision about her powers, while Coulson finds himself going up against... S.H.I.E.L.D.
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.
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.
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.