Alphys was the royal scientist when Asgore was alive. In the teaser fangame, Sans mentioned that she might be dead. In the flashbacks of the comic, it is shown she has went silent. She attempts to fix the Core, but gives up. The first time we see her speak is when Undyne is about to kill herself in Waterfall.
At this point, Alphys reveals to Undyne another power source the Underground could use, possibly to help jump start the Core. She convinces Undyne that they need to do this, for the sake of the monsters.
In the current point of the comic, her status as alive or dead is unknown.