*The color of the sea is depicted as red, instead of being blue.
* Sachiel is attacked by ordinary bombs and missiles, before being attacked with a N² bomb.
* The NERV logo has been slightly changed
* The Seele logo has been changed.
* Shinji wears an ID card on his chest within NERV headquarters.
* The Eva launch sequence is primarily done with CGI.
* Unit 01 now features various glowing, green colored bands.
* Before returning to Misato's apartment, Shinji and Misato go shopping for food.
* Within the convenience store and Misato's apartment, corporate product placement is visible (Lawson Convenience Stores, Frito Lay, Yebisu Beer, Kirin Beer, and UCC Coffee).
* When Shinji and Misato watch Tokyo3 go underground, the scene is primarily done with CGI.
* Shamshel's segmented limbs are completely CGI.
* Unit 01 uses a gattling-gun against Shamsel, instead of a simple rifle.
* After grabbing Shamshel’s "energy whips", Unit 01’s hands are revealed to be composed of humanoid flesh.
* Unit 01's progressive knife is housed in the upper-portion of the shoulder.
* When Shamshel is killed, he entirely liquifies into blood, except for his "energy whips", which remain imbedded in Unit 01.
* When running away from home, Shinji spends a night sleeping in a business district, within a cardboard box.
* Shinji ends up walking to a portion of highway which was damaged by his latest fight, and finally decides he wants to return home.
* After making this decision, NERV agents appear, and return Shinji to Tokyo-3.
* Ramiel is almost entirely animated with CGI, and when attacking or defending changes shape.
* When devising the plan to combat Ramiel, Misato holds a short meeting with the other adults, so they can discuss an effective strategy.
* The preparations for the battle with Ramiel are more involved, and shown with greater detail.
* Shinji explains to Misato that piloting an Eva is scary for him, but it must seem easy to Misato because she observes everything from behind a computer terminal.
* Lilith (said to be Adam) is shown to Shinji, and Misato explains that the angels are attacking Tokyo3 because they want to free "Adam", and trigger a "third impact".
* Touji and Kensuke send a Shinji a message wishing him good luck with his next encounter.
* Before engaging Ramiel directly, NERV utilizes a variety of conventional weapons (missiles, heavy artillery, etc.).
* Shinji hits Ramiel with an initial beam of energy, but it does not kill Ramiel. Ramiel's response nearly destroys the entire mountain which houses Unit 01 and Unit 00.
* Gendou recommends having Rei take the next shot at Ramiel, but Misato objects, and says that Shinji will remember the encouraging words from Touji and Kensuke, and regain his confidence.
* When killed, Ramiel hardens into a spiked-ball and explodes into a rain of blood.
* Shinji uses Unit 01's progressive knife to remove Unit 00's entry plug, so he can free Rei.
* Kaworu is introduced at the end of the film. He rises naked from a box, and speaks directly with Seele 01, and concludes by saying he wants to hurry and meet Shinji.