Coulson continues as director of the new shadow S.H.I.E.L.D. operation, and is forced to hire a group of mercenaries to supplement their efforts. They soon discover that HYDRA is after an artifact from World War II and is employing Crusher Creel--the Absorbing Man--to obtain it. Meanwhile, General Talbot continues his hunt for the team.
While Lance considers a new job offer, Coulson and his people try to track down Creel before he can give the obelisk to Hydra. Meanwhile, Fitz tries to cope with the loss of his partner and Raina reenters the picture.
The reason for Jemma's departure is revealed, as Donnie Gill is discovered and both Hydra and S.H.I.E.L.D. want him because of his ice powers. Meanwhile, Fitz confronts Grant for the first time since Grant tried to kill him.
Coulson and Melinda go undercover to get a painting which may hold the key to Coulson's deteriorating condition. However, when the mission goes source and Hydra sabotages the Bus, Fitz may be the only one who can save the team.
When Skye's father refuses to help her, Raina is forced to threaten Jemma's cover unless Coulson helps her recover the obelisk. When he refuses, Jemma is forced to turn to an unexpected ally to make her escape.
Whitehall hires mercenaries to impersonate S.H.I.E.L.D. and stage an attack on the UN. Coulson sends Melinda, Lance, and Bobbi into the field to find the man who designed their weapons, and then negotiates with the Senator who is calling for an anti-S.H.I.E.L.D. ban: Grant's older brother.
A killer strikes at the survivors of the Tahiti Project, and Coulson must undergo painful memory retrieval to identify the next intended victim. Meanwhile, Melinda, Bobbi, and Hunter follow Ward after his escape from custody.
While Coulson and some of his team head to Hawaii on their first step to locating the alien city, Melinda and her remaining teammates check the SRS records for information on Whitehall and his connection to the Red Skull. Meanwhile, Bobbi interrogates Sunil and Grant abducts his brother and forces him to tell the truth about what happened to their brother Thomas.
Coulson is forced to divide his team, sending half of them to rescue Raina from Hydra. Meanwhile, he leads the other half to San Juan to find the entrance to the Kree city. However, gaining entrance to the city may cost them dear.
Grant takes Skye to meet her father for the first time that she can remember. Meanwhile, Hydra attempts to enter the Kree city and Coulson launches a desperate attempt to stop them... and keep Raina from entering the temple with the Diviner.
As the team deals with the loss of Trip, Skye remains in quarantine to make sure that whatever infected Mack hasn't spread to her as well. Meanwhile, the heads of HYDRA discuss what to do now that Whitehall is dead.
A mysterious woman walks out of the ocean and Coulson's team soon confirms that she's their ally Lady Sif of Asgard. They soon discover that she has amnesia, and that an alien Kree is responsible... and he's there to destroy anyone transformed by the obelisk.
Cal assembles a team of index individuals to help him expose Coulson's "crimes" to the world. Meanwhile, Skye fights for control of her new powers, and Melinda calls in a psychologist and former S.H.I.E.L.D. employee to help.
While Coulson secures Skye at a hidden location, Bobbi and her true masters tell Lance their intentions. Meanwhile, Grant and Agent 33 prepare to break Sunil out of government captivity.
Coulson confronts Mack over his betrayal, only to learn that he's too late. Meanwhile, Skye receives an unexpected visitor who offers to show her how to master her newfound powers.
Coulson and Lance go to ground while waiting for Coulson's reinforcements to arrive. Meanwhile, Gonzales makes an offer to Melinda, Fitz refuses to play along, and Skye meets her new transitioner.
While Skye trains in the city of Afterlife, Melinda takes over her new duties and discovers that Coulson was hiding secrets from her. In the past, Coulson and Melinda go on a mission to recover an Enhanced, and Melinda soon finds herself up against an unexpected enemy.
Skye insists on accompanying Cal home to ease the blow of his losing her and Jiaying forever. As Hydra closes in on them, Coulson initiates his plan to track down Hydra... by allying with Grant and Kara.