The ultimate plan was for all the zetsus to combine into one and form a super special awesome zetsu that will turn on tobi, forcing him to retreat. Naruto and sasuke will fight him off and then talk for a bit then they will begin fighting. Naruto and Sasuke will both be severely weakened and then Tobi comes back to take them both out at once but gets stopped by Kabutochimaru. Suddenly sasuke reveals the scroll that Suigetsu will give him that " could change the tide of the entire war " and eventually sasuke will kill kabutochimaru, thus effectively ending the war, but not the battle. Tobi will then fight with sasule and tobi will gain the upper hand and then naruto will jump in and save him and they will smile at each other and beat up tobi to the point where he reveals who he really is ( a Boo from super mario ) and then he will be sealed. Naruto and Sasuke will continue to fight because its the only way for everything to be put to rest and they will either kill each other or knock each other out
as for the loose ends, The 5 kages will seal Madara, Bee will be gravely injured, Raikage will protect him, everyone realizes that this is narutos fight to fight alone and will back off.