S ranks are primarily driven by how much health you have remaining and the number of stars you have from the quick time events at the end of the fight. Oddly enough, the more stars you get the more health you recover. That said, you'll naturally want all of the stars you can get. Quick time events occur when the character icon begins to flash, so be ready once you see this.
This fight is when Sasuke reaches his older brother Itachi and is facing him for the second time in the Uchiha hideout. As with many fights, it starts out as any normal battle would. Itachi has pretty good defense against normal attacks, however if you throw some enhanced Shuriken (Triangle + Square) you'll find that he'll do the same, bringing up a mini quick time event where you mash Square in order to deal a good chunk of damage to him. After doing this a few times, you'll have your first QTE. The inputs are as follows...
After this cutscene, Itachi summons Susano'o which will drop it's sword on the map in your general direction periodically. Dodge this, and then chakra dash in towards Itachi and begin to break his guard. Simply do this by pressing O repeatedly near him and doing a sequence of melee attacks. Do the same after the guard breaks, and you should receive a prompt to do a good chunk of damage on him.
After doing this, he will use a technique in which rocks fall and you must evade them for a time and he'll drop the sword once again leaving you a window for attack. Repeat this process, dodging the increasing attacks from Susano'o until the time for the quick time event is upon you. Then input the following commands...
Up Triangle Square
After this, you'll simply have to walk back and watch the cutscenes which will lead to your secret factor and hopefully the S rank thus resulting in this trophy!