This is the father of all spoilers, and I may begin to sound like a lawyer at some point.
Most of your soul, apart from the small part (the 'you' in the interactive dream) that stayed defiant against Bhaal (your instinct), was torn from you by Irenicus. When you killed Irenicus in Suldanesselar, your soul couldn't pass on into death, because it was bound to two people. You and Irenicus (the two with possession of said soul) were taken into a limbo state to compete for the soul. You fought Irenicus and won (I hope), rendering him soulless and dead. Then you returned to the prime material plane, soul intact, though probably a fair bit worn out from all the trouble.
The cowled men in the end sequence were old worshippers of Bhaal. The prophecy was that once every Bhaalspawn was slain, their souls would manifest and give rebirth to Bhaal himself. The worshippers are afraid that you are getting too strong to be defeated, thus rendering the resurrection of Bhaal impossible.
A'ight?
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