http://www.evaotaku.com/html/evafaq2.html
Q) What happened in The End of Evangelion?
A) This is a severely abbreviated overview of The End of Evangelion that simply touches upon the important aspects and details of the finale:
SEELE, believing that mankind had become a colony of worthlessness decided that in order for mankind to be happy, all life needed to die ("God, man, and all life must die in order to become one" -SEELE). In the process, mankind would become one in a single, perfect, being. This is the Human Complement Project
Gendo had a different scenario for the Complementation of mankind and his process seems to have included the use of Rei, Adam, and Lillith while SEELE's focused on Eva-01 (direct clone of Lillith), Evangelion Mass Production Models and the Spear of Longinuss (at first intended for the original Spear, but the replicas would have sufficed).
The SEELE version of Human Complement Project appears to have been initiated with the death of Evangelion Unit-02 and the return of the original Spear with the arrival of Eva-01. With these events occurring in the GeoFront, Gendou gave Adam to Rei (Adam is imbedded in Gendou's hand- this is seen quit clearly in the re-vision of eps. 24) and instructs her to take him to Lillith. However "out of her own judgment" she refused and returned to Lillith alone - then putt the future of mankind into the hands of the son of Ikari, Shinji.
When given a choice at the end of Complement Project, if he wanted mankind to return to reality or to complete the project, Shinji decided that a life in reality, no matter how painful, is better than a fake happiness (Kaworu: "AT-Field will harm you and others again, are you sure?" Shinji: "That's fine.") The Mass Production Eva series falls still, their cores break as the Lance Replicas are destroyed.
As the souls of mankind flow back to earth, millions of glowing crosses ascend with Eva-01 and the Lance into the depths of space. Yui caresses Shinji's cheek as they they say their final good-byes. In a flashback, Yui's goal for Eva - as a testament that humanity existed even after the sun, moon and earth are gone - becomes clear.
Shinji awakes up on a desolate beach. Asuka - her arm and eye bandaged in a manner similar to Rei's - lies motionless next to him. Shinji, at the culmination of his love, hate, stress, frustration, etc. - begins to strangle her, only to stop when he feels the caress of her hand across his face. He breaks down, sobbing on top of her.
Q) Which is the true end to Evangelion? The TV episodes or the films?
A) The End of Evangelion is the official ending to the saga. In the RCB it is stated that EoE was created from the original scripts for eps 25 and then a new script written to continue from that episode, but because of production errors they could not be used. However, this does not mean the TV ending is false, it is simply an alternate conclusion.
Truth be told, Darth Utsanomiko and I are really the only two people you need to ask. We know a lot about Eva and we're always right.