After the creation of papyryne, alphys realized what she did, the whole thing hit her at once.

1. She mutated an innocent man

2. Any chance of reviving undyne was gone

3. She has been a terrible royal scientist

   So she ran, she ran all the way to the core, she remembered the way her mentor was lost, and thought it poetic to, well, end it there.

   Alphys became a goner/gaster follower, and replaces the mystery man in this AU