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.
Hunted and running out of solutions, Coulson puts his team right in the line of fire, with General Talbot, Hydra and Creel all on the attack. A mysterious Doctor harbors some dangerous secrets that could destroy one of our core team members.
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 hug him.
While on a mission to learn more about the secrets of the mysterious writing, Coulson finds himself attacked by the only person he can trust: Agent Melinda May. The rest of the team is trapped in an explosive situation, and it's up to Fitz to save them.
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 hugger 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 Mack 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.
Coulson and his team are still reeling from a shocking revelation that leaves the team fractured as they must decide what to do with one of their own. Meanwhile, Bobbi and Mack reveal their true allegiance to Hunter, while elsewhere, Ward and Agent 33 embark on a personal mission.
War comes to Coulson's doorstep in a way he never anticipated as shocking revelations are brought to light, and Skye struggles to control her new abilities but will soon make a decision that irrevocably changes her life.
As Robert Gonzalez makes his move, Coulson must do whatever it takes to protect the future of S.H.I.E.L.D.. Meanwhile Skye's journey to control her powers takes a surprising turn when she meets the enigmatic Inhuman named Lincoln.
The story of Melinda May's transformation into "The Cavalry" is revealed as she finds herself at a crossroads in the war between Coulson and Gonzales. As Skye learns more about her true heritage from Lincoln, the truth about the Inhumans will send her in a new direction.
A dangerous new alliance is formed as Coulson and Hunter turn to the last person anyone would expect - Grant Ward! As the war between S.H.I.E.L.D. factions continues, Skye and Lincoln will find themselves drawn into this conflict.
Gonzales and Coulson must find a way to put their differences aside and work together against Hydra, even if it means teaming up with someone they don't trust.
Skye is torn between her loyalty to S.H.I.E.L.D. and her connection to the Inhumans as tensions rise between the groups - and Coulson reveals a secret he's been hiding from even those closest to him.
Coulson finds himself on the defensive when Jiaying accuses S.H.I.E.L.D. of starting a war on the Inhumans. Meanwhile, Lance and Fitz discover that Grant has captured Bobbi, and Skye questions Raina about her intentions.
Coulson and his team launch a last-ditch attack on the hellicarrier to stop Jiaying from unleashing the Terrigen crystals and wiping out S.H.I.E.L.D.