Board Thread:Wiki Discussion/@comment-27662991-20160123181044/@comment-26887879-20160513195318

GetYourFix wrote: I think the human SOULs may be shattered at the end of geno. Maybe (speculation!) Alphys saw the protagonist committing acts of violence and thought DT was the answer.

To get more DT, she borrows the SOULs from ASGORE without telling him about the dust fest going on. During extraction, the SOULs shatter (we know that they do as much at the end of neutral runs).

That may explain why nobody uses the human SOULs in genocide. ^^' Or they're only accessibly by ASGORE. That's also likely. It might be that Flowey stopped Alphys from informing Asgore about Souls. After all, when doing Genocide he's helping us, it's implied he's the one who deactivates all the puzzles...