Unit 00 was initially colored yellow like the previous prototypes, but its armor was damaged beyond repair by the Angel Ramiel and has since been refitted with blue armor plating in addition to other alterations made in order to make it more suitable for combat conditions including shoulder "Blades" are added to the Unit's armor; though similar in appearance to the ones on Units 01 and 02. Because it is a prototype, Unit 00 cannot be fitted with D-type equipment. Unit 00 is also equipped with retro rockets as shown in the fight against Matarael. The true nature of the soul inside Unit 00 is never specified, but it is implied to be directly connected to Rei in some fashion. Popular theories include the soul of Rei I, or Naoko Akagi (less likely). Unit 00 was destroyed when Rei self-destructed the Eva in order to destroy the sixteenth Angel, Armisael.
In the Rebuild of Evangelion series, Unit 00 design stays with its initial yellow color along with more white and gray. In the second film, Unit 00 was the Eva SEELE recommended be placed in storage upon the arrival of Unit 03, as the Vatican treaty states that no country can have more than three active Evangelion units at one time but Gendo Ikari chose to place Unit 02 in storage instead. Against the 10th Angel, Unit 00 was absorbed after the point-blank detonation of an N² Missile and its identification code was used by the Angel to disable Central Dogma's defenses.