@satoru-raiden already mentioned Evangelion and I think that would be my first answer too, it's so complicated and to be honest, I think no one will ever know what the hell does it mean xD
But to mention another one, Attack on Titan is definitely a mind blowing plot too. Summarize it to someone that has no idea about anime is like explaining the Bible, so many characters and plot twist. It's not simple to understand.
And let's be honest, even the premise itself is kinda strange. It's good tho, but weird hahaha
I am only 2 seasons into AOT, just never went back to it. But explaining the first season isn't too bad, the second is where I lose it ahahah
Season 2 is when it gets complicated, and the more you watch, the more you can get confused hahaah
Although when you get it, is an awesome anime. Hope you can watch it fully someday :)