The full story
The Chronicoms, having failed to conquer Earth by force, settle on erasing the one obstacle standing in their way: S.H.I.E.L.D. itself, going back through history to prevent the agency from ever existing. Using a stolen jump drive that can only travel through specific windows in time, the team follows the Chronicoms across S.H.I.E.L.D.'s own past -- accompanied by a Life Model Decoy built in Coulson's image, since the real Coulson has been dead since Season 5.
In 1931, during the construction of the Empire State Building, the Chronicoms try to stop a young researcher from ever developing the formula that becomes the super-soldier serum -- the same serum that will one day create Captain America. The team also meets Ernest "Deke" Koenig, ancestor to the family of identical Koenig brothers scattered through S.H.I.E.L.D.'s later history, and starts building the earliest version of the agency around him. Jumps to the 1950s and then the Cold War-era 1970s and '80s follow the same pattern: wherever the Chronicoms try to erase a piece of S.H.I.E.L.D.'s foundation, the team has to arrive first and protect it, all while trying not to unravel their own future in the process.
A major complication arrives from an unexpected direction: Daniel Sousa, Peggy Carter's old S.H.I.E.L.D. partner from the 1940s, is pulled forward through the team's own time jumps and ends up stranded in the present alongside them, forming a relationship with Daisy Johnson as the season goes on. The season also digs into the Malick family's role across the decades, introducing Nathaniel Malick, an ancestor of Hydra's Gideon Malick whom the Chronicoms specifically need dead to erase Hydra's rise -- meaning S.H.I.E.L.D. has to protect an enemy's bloodline in order to save its own history, alongside the mysterious Chronicom operative Sybil.
In the finale, Fitz -- reunited at last with Simmons after the pair spent their own subjective years apart perfecting the mission -- engineers a way to send the team back one final time and lock in a new, safer branch of history, one where Daisy's sister Kora survives a suicide the original timeline didn't prevent. Daisy deals with Nathaniel Malick and Sybil directly, while May and Kora work together to talk down the last of the Chronicom-aligned Hunters rather than fight them. With the timeline secured, the team scatters into new lives: May takes over the Coulson Academy to train the next generation of agents; Mack remains S.H.I.E.L.D.'s director; Yo-Yo stays on as his top agent; Fitz and Simmons are finally reunited with Alya, the daughter they spent years planning to have and raise together; Daisy and Sousa head off to rebuild S.H.I.E.L.D.'s next chapter alongside Kora; and Coulson's LMD, still figuring out what he is without ever having been the man he was built to resemble, drives off alone -- leaving open, for the first time, whether he and May might someday find their way back to each other.