The Nerevarine didn't die.
Spoiler The Nerevarine went to Akavir.
There are conflicting accounts as to what happened to Nerevar Indoril. The Ashlanders and Dagoth Ur both claim the Tribunal killed Nerevar. The Tribunal claims Dagoth Ur killed Nerevar. I believe there may be a third account of Nerevar's death but I don't recall it. Like the fate of the Dwarves it's left ambiguous and will probably remain so. Dagoth Ur maintains his story right up to the very end, of course, but he's also thoroughly insane--hardly a reliable source. The Ashlanders and Dissident Priests weren't there. The Tribunal is obviously going to deny culpability. There is no truly reliable source. In this one instance, however, my money is on Dagoth Ur telling the truth--the Ashlanders and Dissident Priests may not have been there and Dagoth Ur may be insane, but the Tribunal certainly had the most to gain from Nerevar's death and the most ulterior motives for their version of the story. Just my two septims.