Thanks for asking! Here's the full story (forgive my bad English)
Physis!Alphys (aka Alphysis) comes from a Horrotale timeline like any else.
We all know what happened. Sans opened her head in half, and then Mettaton tried his best to stitch it up back close.
She (somehow) got a bit better…?
She has no more instinct for self-preservation, her emotions are very confused, she sometimes mutters nonsense, but her intelligence has always been present.
While all of Aliza's adventures were taking place, Alphys kept herself busy building all sorts of inventions. Most of them were useless or stupidly dangerous... but one day, when Undyne arrives at the laboratory, she shows her her latest invention.
A HUMAN CLONE.
She was able to find and enter the world's code, and so clone Frisk's code.
Buuut it wasn't as easy as it seemed, so the clone came out sooo small. It would fit in an adult's palm.
And the copied sprite was from some old data, so the clone had purple/black hair instead of brown.
Undyne was amazed, and requested her… demanded her to create more humans to feed the population.
Alphys immediately stopped her and showed her that for months she has been growing clones of lemon trees that grow super fast.
…Undyne at that point wanted to both punch her and kiss her, but anyway, fact is that she just saved monster kind from hunger! They just had to plant other food.
Time passes, the hunger of monsters stops, Undyne finally regains her popularity, and Sans now tollerates Alphys.
But it all ends when one day a skeletal, glitchy hooded figure arrived, spreading panic throughout the underground.
He killed and destroyed everything in his path.
He was fast and messy in his ways.
He wasn't there to destroy the place. He was there for murder.
His only thought was "KILL. FOR. EXP".
Every time he killed someone he counted, as if he knew perfectly well who was missing.
As if he had done it a thousand times.
That day there was another glitchy skeleton there. From afar he saw the pieces of the codes crumbling and being destroyed.
Panicking he entered the place, hoping to help, and there he met Alphys, who was intent on saving her inventions rather than her life.
He asked her to save herself by leaving the place through his portal, but she instead pushed him through it and threw a box at him, asking him to protect it for her until she returns, and so she ran back to her laboratory.
At that point he couldn't do anything else to save that world.
He heard some banging from inside the box and when he opened it he reveals the little human clone hidden inside.
Not long after, Alphys showed up again, holding all of her inventions in her arms.
The skeleton asks her how she managed to escape, and if she managed to save anyone else, but she replied saying that they are all better dead, and that it's not the first time she left her universe.
Her morals are rather twisted at this point…
She thanked the skeleton, introducing herself as "Alphysis", while he called himself "Basic".
Alphysis and the Frisk clone move to the Omega timeline, where they spend their days creating anything that can help the place's technology grow, without much success since, well, Alphysis will never change.
Frisk, on the other hand, grows successfully, up to 2' 4'' ft!
And now they call themselves simply "Clone" since "H-420", as Alphysis called them until then, was a very difficult and ugly name.
