Alpha gained a soul by developing the ability to care about others and that pushed him to become something more than what he was created to be.

I've never been so moved by a raid story before. Omega has done everything it could to gain strength but eventually realized the kind of strength it lacked was impossible to achieve due to its own flawed design. And when you learn that the only reason behind it all, all Omega wished for, was just to go home… And as it finally starts to attain what it lacks, it disintegrates. It’s interesting that this happens in a way similar to how beings with a soul sometimes turn into crystal dust upon death, so maybe it finally gained some semblance of a soul? At least Alpha managed it and survived to enjoy exploring the world. It was also sad how he behaved towards Omega like a child to its emotionally cold and distant mother.