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Tommen is cremated and his ashes spread over the ruins of the Great Sept of Baelor where Tywin, Joffrey and Myrcella were also buried.
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Later, Cersei visits Tommen's body and orders him to be burned and buried in what is left of the Great Sept of Baelor, saying he should be buried where his grandfather, brother, and sister are buried.
-http://gameofthrones.wikia.com/wiki/Tommen_Baratheon#Season_6