Can somebody please explain to me what happened in End of Evangelion?

It is not something that can really be explained..... The only way to say it is the author was receiving death threats while in the process of writing it (which he actually uses during some of the transitions in the anime. Creepy...) because people were so pissed that the series was actually ending and they were afraid of how he was going to end it. So... he just kinda ended it? It was not explanatory at all. The author did release a statement on the ending. I'm sure if you looked for it you could find it. But there really is no way to explain what happened in that ending. Just as you say, my mind was also violated by it...