A rectangular boat
. According to the book of Exodus
in the Old Testament
received a revelation from God
to load all animals
pair by pair into a huge Ark, thus saving all species from a world-wide flood
. The line spoken by Kouzou Fuyutsuki
in episode 26', "Will it become the Ark to save humankind from the nothingness of Third Impact?"
touches upon this legend.
Source: The End of Evangelion : Glossary contained within The End of Evangelion - Theatrical Program.