Lyric discussion by Jingo7 

Cover art for Goodbye Blue Sky lyrics by Pink Floyd

To me the song is about an atomic war that never happened. The little girl says theres an aeroplane in the sky. Just one? Cant be the blitz but could be a lonely bomber unloading an atomic bomb on london or somewhere. The fact they have to run for shelter with the promise of a brave new world implies running to a fallout shelter and rebuilding a world shattered by nuclear attacks. Goodbye blue sky is obviously saying goodbye to the pre-nuclear world and its clean blue sky and hello to the scorched sky of post-nuclear world. The flames are all gone but the pain lingers on implies the radiation left by the fallout from the atomic bombs and its continuation to poison the post-nuclear survivors.
thats what I reckon.

Totally makes sense. Never thought this way. I'm not good with dates, but wasn't the atomic bomb invented before the end of the WW2? If so, no manage of atomic attack in London could be there