After saving Miss. Peregrine she is badly hurt and needs to rest. They all are finding out what to do to save all the ymbrynes from the wights and hollowgasts..
Eyes were important because wight eyes were all white with no pupils representing they are on the bad side and hunts down peculiars to kill them and ymbrynes to use them for their plan of making themselves gods.
They made up a plan and found out where they were taking them which was far. They decided leave their house and set off on boats to save all the ymbrynes from being killed.