Papyrus startles out of his own wailing by her reaction, rolling over to stare up at her. Did his sadness hurt her? He's already hurt too many as it is, he can't let that happen.

"Oh no! Alphys, no, don't hurt for me...! We mustn't get lost in a recursive loop of sadness, I've already hurt too many... and that's not the kind of person Papyrus wants to be." He reaches out an arm to pat at her reassuringly, but since he definitely can't reach a shoulder from the ground, he just goes for patting at her foot. If he can even reach from here.