Taleshift

I'd dig through my comment history if you can, because I'm basically doing this vertabrim as I haven't been engaged with the project in literal months.
Basically, the AU takes place about 8-10 years after the initial game. In this universe, Frisk wasn't born until 8-10 years after the initial game. Chara never went through with his plan, (I think I was still planning on it being a thing, but Toriel and Asgore found out and intervened before anything bad could happen).
Toriel and Asgore both retired and passed on the crown to Undyne, hence their current residence in Snowdin.
Things were peaceful for a while, but a new child came to the underground. I cannot remember the name for her, but she showed an interest in the scientific arts. By this point, Papyrus was a part of the royal guard and Sans had joined Alphys on the scientific team as a physicist. Sans was generally well loved by pretty much... Everyone. He was a light in the darkness.
The CORE was still being worked on, and this new child joined Sans and Alphys to show them this seemingly powerful marvel - something that might be able to generate enough energy to break through the barrier.
However, anything that falls into the CORE is obliterated from reality, just... Completely gone. This new child, who had a deep seated hatred for all of existence, decided to try and overload the CORE in order to destroy all of reality. The following scuffle killed both Sans and Papyrus, and obliterated the new child from reality in much the same way that W.D Gaster was.
Undyne's grief blinded her. She instituted a new rule that any human who passed through the underground was to be killed, with the exception of Chara as he had grown into quite a good friend to those in the kingdom and was a promising scientist in his own right.
She exiled the monsters who would not follow this decree to Snowdin. Alphys left in shock at her queen's new dark side. The exiles fought with the royal kingdom for a while in a protracted conflict, and eventually Undyne convinced Asriel to join her as captain of the royal guard and Chara to join her as her royal scientist. Chara was the one who created Flowey by experimenting with the remnants of Papyrus.
Meanwhile, Toriel delved into the same research that Sans had when he had helped make the CORE, hoping there might be some way to retrieve him. She's actually stumbled across the existance of this "new child", which has lead to her apathetic nature. Both parents just want their children back, at the end of the day.
The switcheroo I'd intended to make was to have the readers presume that Sans was taking the place of Chara in the AU, and in fact Sans HAS taken the soul of Frisk and is the narrator. The "New Child", however, still exists and wants to destroy all of reality. In a genocide run, Sans' dialogue would eventually give way to the yellow-text of the "New Child", and she would appear at the end.
I am remembering all of this poorly, so feel free to make adjustments to fill up plot holes. It's a little more finickity than a straightforward swap AU, as I'ved dicked with the placements of events.