Off the top of my head, I'd have a Necromantic Cult be the cause of all the undead, and also probably at least part of the campaign motivation. Not a secret cult, but closer to an actual religion, and one that's gobbling up converts at an alarming rate in the hinterlands of Chult. Who's behind this rise in death worship? No one knows, and the priests of the Death God always go masked. There also seems to be an alarming rise in disappearances in the towns where the Cult is active, but a lot of those towns are remote, and the rumors that have reached Port Nyanzaru are wild and conflicting. Priests of Death preach on the street corners of the Port, and rumors of armies of undead swirl in the taverns. An emissary of the Death Cult recently met with the governor of the Port, but no one knows the purpose or result.And if they die what happens. What about all the undead infesting Chult. A great many of the motivations and npcs are tied to Death Curse sites.
But we can just strip all of this away.
That's the broad strokes that I came up with while multi-tasking at work anyway.