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Horcruxes are to Voldemort as Electromagnetic pockets are to MIB.
This would explain why the island isnt finished with Des, because he needs to destroy these horcruxes...err I mean electromagnetic pockets. The rules don't apply to him and he has already shown he is capable of destroying one electromagnetic pocket (swan station).
So if they destroy all the electromagnetic pockets, they will destroy MIB.
Everyone might die in the process, but thats OK because they will live on in the flash-sideways.