Lyric discussion by egger 

Cover art for The Flag lyrics by Barenaked Ladies

I think the "there goes a-" part is a metaphor for the relationship described in the rest of the song. It's a contrast between freedom and security..

Forest = Dark, scary / Blue Bird = Free Partridge = Beauty, freedom / GO Train Confining, controlling Angel = Devine / Steeple = Human Cop Car = Enforcement / Eagle = Soars Free and so forth.

.. So pretty much it's a metaphor for the girl's decision whether to leave him.

If you listen to the drums at the end, it sounds like a millitary march. This could represent her victory or something like that- its open to interpretation.