The full story
A year after Coulson's death, S.H.I.E.L.D. is being rebuilt on Earth under its new director, Mack, while a second team -- Daisy, Simmons, Piper and Davis -- searches deep space for Fitz, who was left behind in cryogenic stasis at the end of last season. They find his stasis chamber empty: Fitz has already woken up aboard a cargo ship with the Chronicom Enoch, and the two of them make their way across the galaxy, eventually crossing paths with a dangerous mercenary named Izel, who buys their freedom in exchange for help finding an artifact back on Earth.
On Earth, portals begin dropping hostile strangers infected with a parasite called Shrike, which crystallizes and eventually kills its hosts while amplifying their aggression. Their leader, a hard-edged figure calling himself Sarge, is identical to Coulson in every physical detail but has none of his memories or personality -- a mystery the team can't easily explain away as a simple resurrection. Fitz and Simmons, reunited but soon captured by the Chronicom leader Atarah, are forced into a shared mental interrogation meant to extract time-travel secrets from their minds, until Enoch -- increasingly conflicted about his own people's mission -- turns on Atarah and frees them both.
Izel's real plan comes into focus: she needs a set of ancient Monoliths to open a passage for her own people to invade Earth, and Sarge, it turns out, is not really a separate person at all. He is Pachakutiq, a formless being from Izel's world whose consciousness became tangled with Coulson's own when it took over his resurrected body, leaving him with Coulson's face and none of his memory. In the climax, S.H.I.E.L.D. fights Izel and Pachakutiq across multiple fronts; May sacrifices herself stabbing Izel to stop her, though Simmons manages to place May's body in stasis rather than let her death be final. Despite glimpses of the real Coulson still buried somewhere inside him, Pachakutiq ultimately embraces what he's become, and Mack is forced to kill him to seal the invasion shut.
With the Lighthouse destroyed by the Chronicoms in the fighting, the team escapes aboard the Zephyr, and Fitz -- as a last resort -- triggers a jump drive that flings the aircraft decades into the past, over Manhattan. In the season's final scene, Simmons reveals what she and Fitz have secretly built to help fight the widening Chronicom threat: a Life Model Decoy of Coulson, rebuilt with alien technology and about to wake up not knowing anything that's happened since his death.