Omg why did he run?!

I want to do my part to nip this discourse in the bud.

Why did Thragg run after his ship got blown up?

Easy. To protect Argall’s skull.

That’s why they gave us a scene showing how much he reveres the emperor, and why they showed him cradling the skull during the explosion. I think it’s pretty obvious that he considers protecting the skull his most important duty.

I’m sorry that we didn’t get a marvel/stranger-things ass line like “I must protect the emperor at all costs!” but I can’t help but feel it’s on you if you didn’t get it.