In the aftermath of The Avengers' battle in New York City, the world attempts to come to grips with the presence of superheroes, gods, and aliens in their midst. Agent Coulson is resurrected under mysterious circumstances and forms an elite team of agents from S.H.I.E.L.D. to keep track of a secret organization known as The Rising Tide. Meanwhile, they must deal with other menaces, such as a man who suddenly finds himself with vast uncontrollable power.
Dark secrets are revealed as Coulson and his team put everything on the line to stop Garrett and the forces of Hydra. But when the dust settles, Coulson will find that no one’s leaving this battle unscathed. And just when all hope seems lost, they’re joined by the one man who may be able to turn the tide–Nick Fury.
Three diehard fans attend a casting session only to find that they have actually just enrolled at the Marvel's Agents of S.H.I.E.L.D.: Academy. Clark Gregg welcomes the new recruits and sends them off to begin the rigorous evaluation process. Do these recruits have what it takes to be a S.H.I.E.L.D. agent?
The Recruit must prove that they are courageous enough for field work as a S.H.I.E.L.D. Agent by completing this high-altitude challenge inspired by Director Coulson’s perilous skydive in the episode “Closure.” Ming-Na Wen (Agent Melinda May) and Henry Simmons (Agent Alphonso “Mack” Mackenzie) introduce the mission. Brett Dalton (Hive) makes a surprise visit and raises the stakes with a devious twist.
In this simulation, the Recruit assumes the role of a newly reborn Inhuman on the run from Hydra. The Recruit must race through an obstacle course and recover coordinates to a S.H.I.E.L.D. extraction point before his time expires. Luke Mitchell (Lincoln Campbell) encourages the Recruit along the way, but Brett Dalton (Hive) adds a high-speed twist to the challenge.
Elena Rodriguez meets with Daisy Johnson privately. The two discuss a secret mission they shared around the time Johnson went rogue from S.H.I.E.L.D. Now that Johnson has returned, Rodriguez wants to make sure their stories are consistent in efforts of throwing off Director Jeffrey Mace. In a flashback, Rodriguez meets with Phil Coulson as he clears out his office after stepping down as director of S.H.I.E.L.D. Rodriguez contemplates signing the Sokovia Accords, but is hoping to seek out Victor Ramon, the man responsible for the death of her cousin.
Director Mace sets a meeting with Rodriguez to have her sign the Sokovia Accords. As she does, she informs Mace about Ramon, who tells her that under the agreement of the Sokovia Accords, Rodriguez has to follow a certain procedure before going after Ramon. Unsatisfied, Rodriguez steals Mace's S.H.I.E.L.D. access card to help her get more information on Ramon.
Leo Fitz and Jemma Simmons examine Rodriguez, during which she secretly learns Ramon is in Baltimore, Maryland. As she sets forth with the mission, she runs into Mack, who is on a mission with Coulson to track down Johnson. As Coulson and Mack's Quinjet takes off, Melinda May informs Rodriguez that Mace's credentials have been reported missing. Rodriguez realizes that May is aware that she took them.
Agent May accuses Rodriguez of stealing Mace's credentials, with Rodriguez reluctantly returning his access card. May advises Rodriguez to be mindful of her "sloppy" work and that she would not tell Mace. Instead, May grants Rodriguez access to another Quinjet headed to Baltimore, allowing her to move forward with her mission. Rodriguez finds Ramon and botches his plans to leave the city. She reminds him that he is responsible for her cousin's murder. As their encounter intensifies, one of Ramon's henchmen knocks out Rodriguez.
Held captive by Ramon, Rodriguez realizes that he is attempting to sell an Inhuman weapon to members of the terrorist organization called the Watchdogs. Rodriguez is rescued by Johnson, who had come for the weapon, and holds off the Watchdogs attacks for Rodriguez to go after Ramon, who had tried to escape.
In light of the Sokovia Accords, and with Hydra obliterated, S.H.I.E.L.D. has been legitimatized again and no longer needs to operate in the shadows. Since the world presumes that Coulson is dead, the organization needed a new Director to be the face of the organization. Coulson finds himself back in the role as an agent and teamed with Mack, and together they are tasked with tracking down and confirming the presence of Enhanced people, aka Inhumans. Agent May is tasked with training specialist strike teams, and Fitz and Simmons have taken a big step forward in their relationship.
Following Coulson's stepping down as Director, Jeffrey Mace is made the new Director of S.H.I.E.L.D. and its public face. Daisy meets with Robbie at his place of work, saying she knows about his history but is surprised to find he isn't Inhuman like her. May's exposure from the specter last episode gets out of hand where Mace, revealing he's a super strong Inhuman, knocks her out and sends her to an undisclosed location. Mack & Fitz investigate the specter and encounter Ghost Rider. The specter who infected May releases her compatriots who were in similar containers for years due to using the "Darkhold".
It was just another average morning on July 22, 1955, when Agent Phil Coulson realized the importance of that day in the S.H.I.E.L.D. history books. With a chip on his shoulder and a genre-bending glitch in his system, he'd set into motion a chain of events that would hopefully preserve the timeline as we know it and ensure those pesky chronicoms get the ending they deserve.
After being unexpectedly stranded in 1982, Mack retreats to his childhood home to process the death of his parents, while Deke gets to work scouting a chart-topping group of new agents. With no idea if or when the team is coming back for them, time seems to finally be on their side ... at least until the killer robots show up.