The fact that freeing him from Medical Mechanica stops them from destroying the world is an unintended side effect. Haruko from FLCL sets the whole plot in motion because she's ( possibly) in love with/wants to eat Atomsk.In Resurrection, it appears that he hasn't even been wearing it, which allows the villain to just walk up and take it. Afro Samurai does not care about the supposed "Godhood" you get from wearing the Number One Headband - He just wants to avenge his father.