Actually dying is kinda mild compared to what I think will happen.
There is actually a second prophecy for the MC. The Gothitelle in the library has a prohecy for you as well. " You will meet the void. It will embrace you. This much is inevitable. What happens after that, however. That, Arceus must not know." If you read Destiny's end than the words Arceus most not know becomes clear. Arceus is actually a succesful deviation of nearly perfect inexistence namely existence. However Destiny's end also claims Arceus will complete itself which means becoming inexistence once more ending the universe as the MC knows it. So what Gotheitelle tells you is that you will become inexistent. Now what has the power of inexistence: well Arceus. However at the moment he is existence so he shouldn't be able to do that. However Team meteor has a way to amplify the latent powers of pokemon: PULSE. So what I think is that Lin will erase us with the power of PULSE-ARC.
Destiny's end also claims that if Arceus does something, it also retroactively changes the past to fit in it's decision within the laws of the universe Arceus made. So when Arceus gave itself a form, the past was rewritten with the events that made this form possible hence the meteor. So if Arceus were to erase us, then the past would be rewritten to fit Arceus' decision. A past will then be written without the MC hence Miss Direction's prophecy.