The way I reconcile the words" I hate you" is that, in my understanding, many WWII veterans spoke very little if not at all of their gruesome experience during the war to their loved ones. The character of Alistair is no exception. He is shown as being adverse to strong emotions, never admitting to losing his temper, proud of having developed a restrain to show anything about himself.
During the course of the movie, he is subjected both to his wife and his son's displays of emotions that upset him greatly. Yet, he never says much about it. He talks about his guilt in a very controlled manner without breaking even though he had carried that guilt for 65 years.
For a man who has sought refuge behind walls he erected, the final plea of his wife is his breaking point. She tells him about her hopes and dreams for them and his eyes are everything but showing hate. The words here are shocking as they are not expected.
This man has dropped his bombs in the wrong village, he has expressed his guilt to the wrong people. He also misfires when he expresses his feelings. Too much has been bottled up. The wife, like the audience is shocked. But the son sees further than this and understands that for a first time at expressing himself it was a start, that in expressing himself in an emotional manner he is starting a healing process.
I personally hear " I hate you for breaking those walls around me and forcing me to come out". Expressing anger at the person trying to help you is part of a healing process. Not an easy one to hear, but 65 years of repressed feelings is not expected to be pretty when it comes out!
Going to Warsaw at the end for me means that the mom finally gets to go where she wants to for once. A big abscess has been broken, the father might still want to get it over with by taking the highway, but it's a road towards healing that they are taking in some poetic way and the son nudges him back by saying they will take the slow road.
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