No, the storyline of Manifest is entirely fictitious; the inspiration for the plot came from the mystery surrounding Malaysia Airlines Flight 370.
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The Manifest season 4 part 2 finale confirmed that 11 Flight 828 passengers died and stayed dead. But which characters didn't come back? The Manifest season 4 part 2 finale resurrected a multitude of fallen characters, but not everyone got a new lease on life.
The second half of season four sees the passengers of the ill-fated Flight 828 — which disappeared for five and a half years back in 2013 before returning with everyone intact, albeit now with the ability to receive “callings” about the future (which actually turn out to be memories, IT'S FINE) — facing down the ...
Flight 828 was a service of Montego Air from Montego Bay, Jamaica to John F. Kennedy International Airport, New York, New York. The aircraft departed on April 7, 2013 carrying a total of 191 passengers and crew. The flight encountered turbulence while airborne and arrived over New York on November 4, 2018.
What's the TL; DR on how Manifest ends? The passengers are back in 2013 and everyone on the plane (excluding Cal) has memories of what they went through. Everything really happened, but now they have a do-over. “We bend over backwards to try to make clear that everything you've watched happened,” Rake said.