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.

The stigmata marks Shinji Ikari as the median of the Human Instrumentality Project, and immediately precedes the occurrence of the Third Impact as seen in The End of Evangelion.

In reality, 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).