To truly understand or be convinced; to have an explanation make sense on a deeper, satisfying level.
彼から事情を聞いて、やっと腑に落ちた。
After hearing his explanation, it finally made sense to me.
数字だけを見ても腑に落ちないが、背景を聞くと納得できることが多い。
The numbers alone don't add up, but when you hear the background, it often becomes clear.
実験結果を確認して、ようやく理論が腑に落ちた。
After checking the experimental results, the theory finally made sense.