Well maybe his spirit escapes his petrified body and found a host to revive himself like he did in tp. and then link has to go to the ruins of hyrule which are now beneath new hyrule and pull the master sword from the souless stone body so he can slay ganondorf for like the billionth time.
actually ganon/ganondorf has died many times and has also come back many times so no i think it's unlikely that ganon/ganondorf is gone for good in fact i somewhat suspect that in the 100 between phantom hourglass and spirit tracks that he may have aquired enough energy to free himself from his...