User blog comment:B214/Best and Worst Final Antagonists in Fairy Tail/@comment-89.242.80.239-20130704132037/@comment-7418318-20130707184143

Brain thought Natsu would make a good servant, so he intended to turn him into an evil subordinate by using Nirvana on him.

Brain could have just ordered Cobra to leave Natsu be, but I guess he judged that Cobra's vulnerbility to loud sounds was too great a weakness for him to still be useful, so he attempted to kill him instead.