For example take sauske.
So before skill breakthrough when you will use sauske's skill it will do damage to 4 ninjas with no buffs and less damage too. After skill breakthrough you can paralyze by using his skill and your damage will be high to i tried him on kakshi.
For skill breakthrough you need book so if you want to breakthrough sauske's skill you need book and you can get it from 100 sauskefregs=1 skill book same for other ninja it requires ninja fregs if you want skill books. you can breakthrough him 2 time he will attack 12units with paralyze but it requires 200 fregs and he needs to be 5*too