SPOILERS!!!

My theory is that the main characters of each of the six stories of Cloud Atlas actually die at some point in their story, but they don't know it. The rest of their story after that point occurs in their afterlife.

Pacific islands, 1849:

The character Adam Ewing is killed by a brain parasite. In his afterlife, he is saved by a stowaway slave, and is evenutally reunited with his wife (whose transmigrating soul may have passed into the afterlife in a different story). A Christian might argue they are reuinited in Heaven.

Edinburgh, 1936:

The character Robert Frobischer commits suicide. In his afterlife, his sould is transplanted onto a rare vinyl record in the form of the Cloud Atlas Sextet, found years later by Luisa Ray. A Christian might argue Frobischer's soul is in Purgatory permanently, or maybe even Hell.

San Francisco, 1973:

Luisa Ray's car is run off a bridge by Bill Smoke. Her soul passes into the afterlife at that point. In her afterlife she goes on to follow in her father's footsteps, working to break a big story as a journalist. A Christian might argue her soul went to Heaven.

London, 2012:

Timothy Cavendish has a run in with debt collectors. I'd argue they actually kill him when he's unable to pay back his debts, and his soul ends up in Purgatory, when he ends up trapped in a nursing home. His soul eventually escapes Purgatory and he is reuinited with an old lover in Heaven.

Neo Seoul, 2144: Sonmi 451 speaks her Orison to the world and is captured and executed by Unanimity. She is a martyr who is a religious figure in the later story. She passed into Heaven (and was possibly reunited with Adam Ewing in Heaven?).

Big Island, 106 winters after The Fall (2321):

Zachry is killed by the Kona tribe in the scene in the forest while Old Georgie is haunting him. His soul goes to Heaven and he goes on to have grandchildren with Meronym.