The song describes Yoongi’s inner war between trying to erase his unpleasant, painful memories and bringing them back in order to cope and use his amygdala to protect himself.

Amygdala is a part of the neural system responsible for processing fearful and threatening stimuli, and activation of appropriate fear-related behaviors in response.

Explaining the writing process for the song, Agust D talked about it in his Disney+ documentary Suga: Road to D-DAY:

In a way, we’re responsible for all our own wounds and scars. No one can dodge the first arrow of trouble, of course, but when that second arrow flies at you, you’ve chosen to just stand there and get hit, rather than learn from the first time. That’s what I wanted to talk about when I was writing “AMYGDALA”.