Synopsis

The End of Evangelion is an alternate version of the final two episodes ofNeon Genesis Evangelion. The first half of the movie is the alternate episode 25, which is called "Air". With all 17 Angels destroyed, NERV and Gendo Ikari now hold all the cards. Possessing Rei, Eva Unit 1, Lillith, and Adam, Gendo can now initiate his own version of Instrumentality (Third Impact). However, before Gendo can realize his dream, SEELE uses the Japanese Strategic Self-Defence Forces (JSSDF) to launch an assault on NERV itself.

The second half of the movie is the alternate episode 26, which is called "My Purest Heart for You". Third Impact is initiated as Eva Unit 1 is put into use for the last time. As the pilot of Eva Unit 1, Shinji controls the fate of the world.

Full Recap

First Part:

SEELE decides to invade NERV Headquarters first by entering the MAGI system. But Ritsuko, who has been released, stops it and later returns with a great army. The base is destroyed quickly as Asuka is sent to a deep lake inside Unit-02.

Rei has dissappeared and Shinji has lost his will to live. Misato rescues him from several soldiers and dies shortly after. Fuyutsuky mananges to stop the army from entering to the headquarters as Ikari goes with Rei to Dogma. Ritsuko waits them there and plans to blow up the entire headquarters, but MAGI doesn't allow her and therefore Ikari kills her.

Asuka awakens after learning her mother's soul is inside Unit-02. She beats the army easily but the Evangelion produced in mass appear and destroy Unit-02 easily, killing Asuka. Shinji sees this inside Unit-01 which goes berserk.

Second Part: 

Eva-01 summons the Longinus Spear from space which returns to Earth. The other Evangelions begin to use Anti AT-Field in order to start the Third Impact. Rei betrays Ikari and having Adam into herself, she becomes one with Lilith. This finally awakens Lilith, who uses Eva-01 and the Spear to bring all the souls into the Door of Gauf, making the Impact occur and erasing all life on the planet.

Shinji is the only one who still lives inside Unit-01 but he decided along with Rei and Kaowru to return to Earth, accepting reality. Lilith allows all the souls to be set free and Shinji and Asuka are returned to Earth. It is a new beginning for the humanity...