S-Ranking a Mission requires 90% or better in each of the categories at the end of each match within a story section. These are usually % Health left, Continues used, % QTE complete. Bonus objectives and time spent have no bearing.
Health must be 90% or better (you will kick yourself the 3rd time in a row you finish on 89%)
Continues are self explanatory, don't fail the fight for a S-rank.
QTE are the various scenes that play out at the beginning/end, you'll know when these are happening as Stars appear at the top middle of the screen.
There are also various in-battle QTE which while not counted, generally stop you from taking massive damage/dealing out extra.
This Mission has 2 battles
Naruto and Killer Bee vs Madara
Just a straight battle here make use of the swapping out with killer bee and chain combos with a Ninjutsu at the end, no QTE or secret actions to worry about.
Keep attacking though and don't let him awaken, otherwise you'll have to deal with Perfect Su'sano.
Kakashi, Naruto and Guy vs Obito
Another straight fight without QTE or Secret Factors thankfully.
keep up the combos and swap in and out for maximum damage, be wary of the amount Obito can teleport. It is somewhat easy to lose him and get caught in a jutsu or throw.