Spoiler: Fate/Stay Night+Unlimited Blade Works
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Unfortunately, Gilgamesh never recovered after Shirou whipped the smug off his face and beat the snot out of him for being a whiny useless git. His ego destroyed, the throne of heroes rejected what was left of Gilgamesh and none have seen him appear since.
Just my personal opinion Looking forward to the remake and next movie, hopefully this time the movie will be a bit more coherent.