So, I've cleared all the nodes and have all 4 gems. I've now noticed that I don't have the skull anymore. I have no idea what happened. Do I need that skull? Feels like I found it a long time ago and I'm not sure what happened to it. I may have put it in my extraplanar chest. Am I supposed to have that skull?
Short answer: no. But the end fight is a bit easier if you can destroy the skull, which you need all the gems for.