Having one of their three strongest warriors taken out so unceremoniously dealt quite the blow to the pirates, not only by literally taking out one of their strongest, but also by simply making them realize that they were outmatched.
If we had people who could come out of seemingly nowhere and take out their leaders, what exactly would happen to these rank and file pirates that were just trying to make a living, albeit through rather nefarious means?
I could see those thoughts running through the minds of quite a few of the pirates already, and when Captain M'Koli Valigeaux raised her blade and shouted "Any who throw down their weapons will be given leniency in their trials!" the resolve they had to remain loyal continued to waver.
Professor Mira stepping forwards and summoning a rather large amalgamation of crackling lightning sealed the deal immediately, with four pirates instantly kneeling down and throwing their blades aside as they surrendered.
