Full story
Season 6 picks up a year later. Mack is the new director of S.H.I.E.L.D. and May is training new agents. Daisy, Simmons and a small crew are searching space for the frozen Fitz. On Earth a man named Sarge shows up, identical to Coulson but cold and violent, hunting parasitic creatures called Shrike. In space, Fitz wakes up beside the Chronicom Enoch and gets into trouble on a gambling planet, until he falls into the hands of Izel, a body-hopping alien.
Izel wants to use the monoliths to open a portal and bring her people to Earth. Sarge turns out to be Pachakutiq, a being from another dimension who got Coulson's face and some of his memories when the team used the monoliths. Fitz and Simmons reunite and even have to face their own minds to survive the Chronicoms. May is wounded by Sarge, seems to die and comes back through the Fear Dimension. In the end, May kills Izel and Mack finishes Sarge, closing the portal.
But the Chronicoms, whose planet was destroyed, want Earth. They attack, and the team escapes on the Zephyr, which can now travel through time. Simmons reveals her hidden card: a new Coulson LMD, upgraded with Chronicom tech. In the seventh and final season, the team jumps to New York in 1931. The Chronicom Hunters, led by Sibyl, want to change history and wipe out S.H.I.E.L.D. before it's born.
The chase spans decades: Prohibition, Area 51 in the 1950s, the 1970s and the 1980s. Along the way the team saves Daniel Sousa, the agent from Agent Carter, who joins the group and grows close to Daisy. Nathaniel Malick, heir to a Hydra family, steals Inhuman powers and allies with the Chronicoms. Kora, Daisy's sister, appears in an altered timeline. Deke gets stuck in the 1980s and builds his own S.H.I.E.L.D. Fitz finally returns in the last episodes and reveals that he and Simmons have a daughter, Alya.
In the end, Enoch sacrifices himself, May and Kora give the Chronicoms emotions and the threat is over. Deke stays in the alternate timeline as director. One year later, Fitz and Simmons are raising Alya, May teaches at the Coulson Academy, Mack runs S.H.I.E.L.D. with Yo-Yo, Daisy travels the stars with Sousa and Kora, and Coulson sets off to see the world. End of the series.