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.
Coulson and team come to the aid of a confused Lady Sif, who has lost her memory after fighting with a mysterious warrior, whose true mission will send shockwaves through S.H.I.E.L.D. Meanwhile, Bobbi and Mac continue to hide their true mission from everyone close to them.
Cal seeks revenge on Coulson by assembling a team of Super Villains to destroy S.H.I.E.L.D. Meanwhile, May calls on renowned Dr. Andrew Garner, her charismatic ex-husband, with a crisis that threatens to tear the team apart.