Naruto and Sasuke are going to beat the piss out of him together with their new powers along with help from the alliance. This whole manga has been about parallels and learning from the mistakes of the past. The sage's sons getting things wrong, Hashi and Madara getting things wrong, Juraiya chasing after Orochimaru and giving up.
Naruto chasing after Sasuke but not giving up has already changed things. Naruto's stubborn refusal to not give up on him is why Sasuke has an opportunity to make up for past mistakes. Naruto is the reason why K11 is tolerating Sasuke instead of going after him. I agree with Jaded Artiste though, they will work together but Sasuke will probably be the one to finish him. Madara will only be defeated with teamwork.