Board Thread:General Discussion/@comment-4383275-20160827054600/@comment-27701762-20160827140308

I wouldn't ascribe the name "villain" to Alphys. One can definitely fault her decisions and actions, but at no point does she actually act antagonistically toward the protagonist (any barriers that she puts up are specifically made so that she can knock them down), nor does she do anything that is actually evil.

As Fix already noted, her knowledge about Flowey is limited to at most a sort of vague knowledge. She had no idea going in what the result would be of creating a being without a soul, nor is she aware of Flowey's malevolence. While Alphys is the cause of Flowey's existence, the responsibility for it is not cut and dry, since she did not and could not have any idea that the experiment would actually work or what would come of it.

Hiding the Amalgamates is essentially the same as her reactivating the puzzles. She was being selfish. In the former case, she was afraid of what people would think about her if she not only failed in her experiments, but returned the family members in such a deformed state. So she hid them away. Likewise, she wanted to feel like she was a hero and part of the protagonist's adventure, so she turned the puzzles back on so she could save the day. She reasons like a child. That doesn't make her bad, per se. Just not good, either.

Alphys doesn't really qualify as a villain, unless "villian" is simply defined as "someone who blocks the progress of the protagonist in any way." She certainly isn't the True Villain. She's just complex, much like Asgore.