- Carl Creel is sent after an item that was stolen from Hydra during WWII. Fitz tries to cope with his mental issues.
- Coulson and his team are now wanted fugitives with limited resources - but that's not stopping them from keeping the world safe from powerful and unseen threats everywhere. However, with new members they hardly know, will S.H.I.E.L.D. ever be trusted again?—Jiilo_Kim
- Flashback to 1945, where Agents Peggy Carter, Dum Dum Dugan, and Jim Morita of the Strategic Scientific Reserve (SSR), an early S.H.I.E.L.D, attack the last known Hydra base following the Red Skull's defeat, arresting the Hydra agents, with their leader, Reinhardt. While confiscating all Hydra weaponry and technology they find, SSR finds a blue body and the mysterious Obelisk.
Back in the present day, former S.H.I.E.L.D. agent Browning attempts to sell information regarding the Obelisk to Agent Hartley and her mercenary accomplices, Hunter and Idaho, who are working undercover for S.H.I.E.L.D., when Browning is killed by Creel, a superhuman that absorbs the properties of anything he touches, changing his molecules to that substance.
At the Playground, the former SSR base that now serves as S.H.I.E.L.D.'s headquarters, Coulson knows the importance of the Obelisk, since it was the first 0-8-4, an object of unknown origins and sends Skye to talk with imprisoned Hydra agent Ward, who has been suicidal and will speak with Skye alone. Ward reveals the secret frequencies Hydra communicates with, and Agent Koenig intercepts Creel's next move, using the family of Brigadier General Talbot as hostages to locate the Obelisk. Agent May, Skye, Hunter, and Hartley help Talbot fight off Creel. Then, in turn, the Agents abduct Talbot, getting the access codes for a U.S. military base containing confiscated S.H.I.E.L.D. resources.
All S.H.I.E.L.D. operatives infiltrate the base, where Agent Triplett poses as a U.S. general. Hartley locates the Obelisk, but is attacked by Creel, until he flees when seeing that the Obelisk is killing Hartley. Hunter, Idaho, and the dying Harley flee with area in an attempt to save her life. Meanwhile, May, Triplett, and Skye follow Coulson's orders to hijack a quinjet. Realizing that she will die before they can get medical treatment, Hartley makes Hunter amputate her arm, since she cannot release the Obelisk. When Mack asks Coulson why he risks lives to steal a quinjet, Coulson explains the need to disappear, which they cannot do themselves following Fitz's injuries suffered last season. Coulson reveals that Fitz still struggles with technology and technological terms, and hallucinates Simmons' presence, who quit S.H.I.E.L.D. because of Fitz's issues. Unable to prevent the car that he, Hartley, and Hunter are in from hitting Creel, Idaho can only watch as Creel adopts the material of the road before impact, which causes the vehicle to flip. As Creel steals the Obelisk for Sunil Bakshi, his boss, it is revealed that Hartley and Idaho were killed in the crash.
Ending Sequence: Bash is revealed to be working for Reinhardt, now known as Daniel Whitehall, who has not aged since 1945.
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