undertale-science:

Alphys is suicidal. Without Undyne, she would have killed herself. If Mettaton dies or Undyne dies she does kill herself unless you get the near genocide ending. It’s something that a lot of players never understand despite all the dialogue and direct hints.

When you call Undyne in the dump she talks about how she first met Alphys in the dump staring silently and contemplatively into the abyss. Undyne talks to her about what’s down there, and Aphys gets to talk about all her theories, and their friendship begins. If Undyne never talked to her, she would have jumped.

She says the above dialogue during the true lab.
If you kill Mettaton and go back to her Lab, it’s closed and there is no response. She has committed suicide.
On the Mettaton neutral ending, he admits he didn’t treat Alphys very well, and when he went back to apologize and ask for her help leading the underground, but he couldn’t find her anymore.

In another neutral ending, Undyne is depressed after Alphys commits suicide and Asgore is killed. Papyrus begs you to bring her friends back from whatever you did to them. But it’s too late. Alphys is the only main character you cannot fight or kill directly (Sans being actually dead after losing the fight is debatable). The only way to kill her is to cause her to commit suicide. It’s one of the darkest thing you can do in the game.