I thought I had a pebble in my sock
I pulled it off and shook out a wasp
It stumbled out lost, and without a pause
I'm stung as I was, still I stomped it
The narrator thought he was dealing with a minor annoyance, like a pebble in his sock, that turned out to be a much greater threat — a wasp.
However, that threat had yet to be realized; he was still ‘unstung’. Therefore, he could’ve just let the wasp live, now that it was out of his range, especially since it didn’t seem very threatening in the first place — ‘it stumbled out lost’. But instinctively, he stomped it to death, anyway.
If we apply this metaphor to the rest of the song, it becomes one for his relationship: it’s getting stale and irritating and he wishes to rid himself of it, but as it turns out, it wasn’t just irritating; something dramatic happened. His partner seems to have done something unforgivable, as the refrain implies (perhaps threatened to leave him?).
So he stomps.
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