It is probably a reference to the rainbow that appeared after the Biblical flood:
- I set My bow in the cloud, and it shall be for a sign of a covenant between Me and the earth.
- It shall come about, when I bring a cloud over the earth, that the bow will be seen in the cloud,
- and I will remember My covenant, which is between Me and you and every living creature of all flesh; and never again shall the water become a flood to destroy all flesh.
- Genesis 9:13~15
God's "bow" being a sign of a "covenant" between himself, Earth, and all living things recalls the mysterious Covenant with Lilith. It's been suggested that the rainbows appear in the wake of Angels' deaths (which unleashes "floods" due to their bodies dissolving into red fluid) as a sign that the covenant is being fulfilled.
Furthermore, rainbows appear upon the destruction of certain Evangelion units, but there is no clear pattern. Eva-04's explosion in Evangelion 2.0 tentatively included a rainbow earlier in production, but this was omitted for the final film.
Aside from rainbows themselves, rainbow motifs are scattered throughout both Rebuild and Neon Genesis Evangelion.
- New American Standard Bible