She worked as a intern for Gaster, helping and observing his expeiments. She was a great pupil to him, so he gave her the job of building Mettaton Extreme, the new body for Mettaton who died in the first raid. During this time, she developed a romantic relationship with Undyne, eventualy merging their souls. After the events of Gasters accident, she became worried for him, and soon began poking into his affaires, trying to find his reason for the change. Gaster soon became angered by her searching, and confronted her. He couldn't let her continue poking int it, and used the orbs of Hate and Integrity. Creating a soul trait that pushed Alphy's soul out. The aspect of solitude. She soon became distant and broke the bound with Undyne, and became a hermit in her lab, never stopping her work, creating robots, technology, and weaponry. Undyne blames Gaster, and still makes attempts to contact Aphys, but to no avail.
Alphys looks very thin and tiered, from never stopping her work. She wears her original lab coat, but it is dirty and covered in oil. Her scales have miscolored and her eyes have become bloodshot.
She has no magical powers, but the twisted and half finished creations around her lab will mob and attack anything that attempt to hurt Alphys.
She is a hermit. She has never stopped working in 3 years, and has never left it either. She is very cut off, never talking to anyone in person, only thru a loud speaker or a robot. She does nothing but work, she has burned every anime item she has, due to it being a distraction from her work.