The phrase in the end means "finally". It is normally used when you want to give the impression that a conclusion was arrived at after a lot of confusion or uncertainty. For example: In the end, the hero runs away with all the money. Hope this helps :)

AT THE END literally refers to the end of something like a book or a movie, for example: "It was a very sad book/movie - everybody died at the end." IN THE END is a little more abstract. It refers to a conclusion in the final analysis of things - especially if there were several twists, turns, and hardships along the way: "Michael had to work two jobs, mow lawns on weekends, sell his bike and skip a lot of meals, but in the end he got what he wanted - the car of his dreams." (Если вы говорите по-русски, AT THE END - в конце чего-то; IN THE END - в конечном счете)