Can someone explain the plot of FLCL and Big O?

Big O has no plot.

Season 1 = Japanese Batman.

Season 2 = Film sets and TOMATOES.

That's all you need to know.

 The truth. Open at your own risk.

The entire series is actually a metaphor for women's frustration with the world and their desire for the perfect orgasm. Watch it with that mind. It's going to change the whole show for you, and I guarantee you'll laugh every time he cries out "Big O."