Alphys is one of the main characters in Undertale and the only character of the main cast that cannot be directly killed by the protagonist. Although she is never shown to die on screen, it is heavily implied that she has suicidal thoughts, ("That's where I met Alphys for the first time!! I was looking for cool swords, when I saw her... Uh, standing there, staring into the abyss. She looked pretty... Um... ... contemplative.") and if both/either Mettaton or Undyne is killed, she cannot be found by the surviving cast members with the exception of in an aborted Genocide Route playthrough.
She has had a former crush on Asgore and is in a relationship with Undyne. In the True Pacifist Route, she decides to show her feelings for Undyne, and they start dating on the surface.
She is the Underground's Royal Scientist.
Alphys is the Royal Scientist and the guide to the player throughout Hotland. She 'assists' the player throughout Mettaton's puzzles and The CORE, which are revealed during Mettaton EX's fight to be activated as part of a ruse for the player to judge Alphys as a hero.
In her career and research of the power of Determination, she accidentally creates the Amalgamates by injecting Determination into monsters to see if it could revive them from death. They ended up melting together and forming beings called the Amalgamates. During this time period, she injects Determination into one of the golden flowers of Asgore's garden. Flowey is born from one of these flowers because of Asriel's dust being spread over it. Thus Asriel it "reincarnated" as Flowey, bit without a soul.