Hayley Williams recently did this interview and in it she said that Josh came up with riff, and everyone liked it so people came up with their own parts on the spot, they got it recorded and hayley took it home and started putting lyrics together.
She says that this song is about the band. And when they were having problems as a band (when they cut the european tour short) and how these problems are still there within them, and this was how she felt.
She also states that putting together Brand New Eyes, was the best theraoy they could have gotten as a band, because it made them see each through Brand New Eyes.