Q: In Sakura’s Route, what happened to the devoured Gilgamesh? Saber was blackened and enslaved, but was Gilgamesh’s will too strong to be dominated? Or was he completely digested?

A: He simply cannot be controlled. In fact Gilgamesh cannot be blackened. After being devoured by the Grail, Sakura converted Gilgamesh into mana in haste because she was afraid that Gilgamesh might tear her up from the inside if she does not digest him. However, His Majesty was very hard to digest, so “Angra Mainyu” must have been plagued by belly-ache (laughs).

Fate/complete material III; FAQ, pg. 130-131