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The beginning of the movie takes place right at the end of episode 24, right after Shinji kills Kaworu. So the beggining of episode 25 and the movie are releativly similar... it isn't til the end of episode 26 that Shinji goes all "happy"
Okay... when attempting to understand the ending of Evangelion it is best to view the TV series ending and the movie ending as two seprate endings... because that's what they essentially are.
The TV series ending which was made in 1995, was the original intended ending for the series, but the fans didn't like it, and chucked up a big stink about it... and so rumour has it, Anno made a different ending, End of Evangelion (1997), which was made to be a big "up yours... you want another ending here you go!" to the fans.
The ending of the series/and the movie deals with the Human Completion Project (ie: Third Impact) which was all about merging the souls of humanity, evolving to the stage where humanity exist as one single being. (the whole merging of AT Fields... blah blah) Shinji, and Unit 01, have to choose whether mankind will evolve, or not.
In the series Shinji sticks with Third Impact, a happy world with no AT fields, no pain and no rejection. But, in the movie he reject Third Impact entierly... releasing that staying with completion was nothing more than running away from reality for it was a fake paradise, with fake happiness where no one really existed as an individual. So at the end of the movie Shinji is still miserable, but at least he's grown up a tiny bit and didn't run away.