A Nautilus green & black flag ? She has never seen that before.
And she has never heard of pirates using non-lethal force in a boarding action. That means one thing : they are looking for something on board. Or
someone.She immediatly became invisible, hidding cautiously where she can, behind ropes and destroyed crates, trying to keep the shadowy figure in sight.
This man can stop someone cold in his track, with a mere flick of his wrist. That means potent magical powers; and it is confirmed by how terrified the pirates are. If there is something that can make a blood-thirsty sea scoundrel quivers in fear, it's magic.
And the best way to fight magic, is using some as well. She took a deep breath, and through mental triggers, unleashed one of her own powers.
She will need half a minute to read the minds of those in front of her. But that's the safiest way for her to learn who they are and why did they attacked her ship.
She uses one of her 1/day Detect Thoughs, save DC 22