Stigmata

In The End of Evangelion, during initial stages of the Third Impact, Evangelion Unit-01 is marked by Evangelion Units 05-13 with what SEELE calls the 'holy stigmata'. Lilith is also crucified in such a manner in Terminal Dogma.

Stigmata (plural of stigma) is a religious term referencing the wounds suffered by Jesus Christ during his crucifixion in the New Testament of the Bible. Such wounds typically appear on the hands/wrists, feet/ankles, and on the side (which according to the Bible was inflicted by the Lance of Longinus).