I love the ending when The Master tells Freddie, “If we meet again, in the next life, you will be my sworn enemy and I will show you no mercy.” Then when he sings that song it sort of elucidates the intricate relationship of power and submission between Master and Freddie. It does present this tendency in people to be subjugated to an ideology in order to find peace with themselves. And Freddie was the guy who was unable to be compliant, yet at the same time, both Master and Freddie are very much alike. Maybe Freddie's presence throughout "The Cause" brought a primal and somewhat childish side out of The Master that had been lost some time ago. A good example would be the scene where Freddie returns from prison, and they see each other for the first time since behind bars as they tackle each other to the ground, laughing while Hoffman slaps his butt. Apparently, that whole thing was not part of the script! it just happened, which kind of gives it a more authentic vibe or something.
I could go on about it, I just love how PTA makes films with heart, and doesn't really sugarcoat his work. It does challenge you a bit. I still don't fully "get" the ending where The Master sings that song and says to Freddie, "If you leave here, I don't ever want to see you again". It's mostly because both have maintained the same level of gratification. He doesn't say it out of malice. My interpretation was that Freddie's inability to be "tamed" to that ideology, as well as his effect on The Master's behavior was sort of detrimental to the whole cause. It only seems to spiral downward, especially when Master is taken to jail. It's basically a seasaw effect.
I don't know, a lot of people I've spoken to found the film disappointing. I did too the first time I saw it... but it has gotten better with each watch for me. Also, I found the acting performances and the music very moving.