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In UBW, when Rin removes Shinji from the Grail, the Grail attempts to take him back (with little hands). Then it grows a massive hand, but instead of going for Shinji, it goes for Gilgamesh to replace its core. Why didn't the hand try to retake Shinji, if he was much closer than Gilgamesh?

One could argue that Gilgamesh would be much more fit to be the Grail's core, but I'm not sure if that's explicitly mentioned or not. Besides, Shinji's body was doing the job just fine I think.

  • Most likely it could be because Gilgamesh was already tainted by the Grail after the 4th War so the Grail, or more accurately Angra Mainyu, went for something similar too it. though i am pretty sure in the game this didn't happen but all i remember was that Gilgamesh was suck into a black hole and tried to take Shirou with him and the black hole was the result of Saber having already destroyed the grail – Memor-X Jul 3 '15 at 0:34
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I'll offer a few reasonable-sounding hypotheses. Some of which I can support, but others I can't. Maybe one of us can then find some evidence to either support or dismiss the others afterwards and thus post a more solid answer.

  • The grail is acting instinctively. It goes after Rin/Shinji first because they're closest. But then it gets attacked by Archer, and decides those two must be too dangerous. It then moves to the next closest target: Gilgamesh.

  • After the Lesser Grail is destroyed, its targets are now limited to things it has a connection to. Gil, being a nearby servant with a physical body produced by the mud, is the only option left. Thus, even though it got curb stomped the first time around, its only choice for survival is to go after Gil. It may also be aware that Gil is weakened and injured, and so expects less of a problem.

  • Shinji's body wasn't really doing "just fine". Rin remarks that the giant fleshy mass is a result of Shinji being too poor a vessel to really contain the Grail. He was only "just good enough" to get the ball rolling. We know in the HF route that vessel there has no real problems containing the grail.

  • On the second attempt, Gil admonishes the grail for apparently not being aware that a servant can't serve as its core. In particular, this would mean that Gil is actually not suited to be the core at all. This could be more evidence of the grail's instinctual behavior: it is either too stupid to have reasoned behavior, or it is so desperate that it's willing to gamble that it can make it work somehow (or buy itself time to find a real solution).

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