The full story
An unknown force pulls Coulson, May, Daisy, Simmons, Mack and Yo-Yo through a Monolith and drops them on the Lighthouse, a space station in orbit around a shattered future Earth roughly ninety years ahead of their own time. The planet was destroyed generations earlier, and the Lighthouse's Kree overseer, Kasius, runs the station by breeding and trading captured Inhumans and staging death-match "Renewal" ceremonies to keep the surviving human population in line. The team meets Deke Shaw, a station-born scavenger with a hidden connection to Fitz and Simmons, and starts working toward a way home while trying not to change a future that, they gradually realize, involves people they already know.
Left behind in the present, Fitz is captured and interrogated by General Hale before escaping with the help of former agent Lance Hunter and locating Enoch, the alien being responsible for the team's disappearance. Enoch reveals a prophecy from a young Inhuman, Robin Hinton, whose visions predicted the abduction -- and shows Fitz that reaching his friends means entering cryogenic stasis for over seventy years to arrive in their future at the right time. He does exactly that, waking aboard the Lighthouse and using his wits to earn Kasius's trust as a black-market bidder.
On the station, the team discovers Kasius has been experimenting on captured Inhumans in search of a perfect specimen, and that a young Inhuman named Flint has the gravitonium-based ability to recreate the Monolith that could send them home. Escaping to the ravaged Earth's surface during a catastrophic gravity storm, they reunite with an aged Robin, who reveals what she's foreseen all along: only by returning to their own present and changing what's coming can this future be avoided at all.
Back in their own time -- having been gone only hours by that point's clock -- the team learns General Hale is secretly working with Hydra remnants and an alien coalition called the Confederacy to build "Project Destroyer of Worlds," a gravitonium-powered weapon meant to intimidate Earth's enemies ahead of an anticipated invasion by Thanos. Hale's own daughter, Ruby, attempts to bond with the gravitonium herself and is killed by Yo-Yo in the confrontation, at the cost of Yo-Yo's own arms; General Talbot absorbs the gravitonium instead, and the substance's residual consciousnesses -- including old enemy Ian Quinn from earlier in the season -- slowly drive him into an unstable, increasingly powerful Confederacy pawn calling himself Graviton.
In the finale, Daisy injects herself with an old Centipede serum to gain the strength to stop Talbot, blasting him into orbit before he can devastate Chicago -- at the cost of gravely wounding Fitz in the process. With no way to save him in time, Simmons instead finds present-day Fitz still alive in cryogenic stasis aboard Enoch's ship, unaged since the season's start, leaving a way to bring him back properly later. Coulson, dying from the toll his earlier bargain with the Ghost Rider took on his body, refuses a serum that could save him and chooses to spend his remaining time with May instead, stepping back from S.H.I.E.L.D. for good as Mack takes over as director.