OK, so Madara shows up and everyone is all "shit got real", he and Obito have a short discussion in which Madara calls him a pathetic piece of crap and plucks out his Rinnegan because he needs it. Obito is all like "shit no!" but he's a one trick pony so completely and Madara being the best of all Uchiha completely negates the phasing tech because he's ultimate. Obito spends the next little while on the ground, bleeding from the face.
Madara then addresses Naruto and the Kyuubi and they go into some shit about world domination and how Madara will reclaim the fox from Naruto. Naruto is all "nuh-uh" and foolishly tries to attack but Madara, being Madara, completely brain fucks him and the Kyuubi - he's had that control in the past - and Kakashi and Gai are all "Ohshit" and tries something but fails. It falls to Bee to intercept in Eight Tails form, which he does successfully to save Naruto and Kyuubi but because his focus is saving, Madara completely owns him and Bee dies, releasing the Eight Tails which is then subdued and captured by Madara, tossing it into the 'Juubi/Gedo' because with Rinnegan he can control that shit.
Things look bad and BOOM Sasuke, Orochimaru and the other two douches arrive. Theres a bit of a conversation about what this all means and the nature of the Sharingan being a corrupting force. Madara sees the power in Sasuke and wants him to join forces to renew the clan, basically because Edo Madara has no sperm and needs Sasuke to fuck a bunch of bitches. He almost has Sasuke when, because they are dumb shits just standing around and forgetting who's with them, Orochimaru initates a final jutsu in his form and captures Madara's edo body and takes over.
FINALLY Orochimaru, the best villain in this shit, gains the body he wants and it is better than anything he could hope for. He's got Rinnegan and is immortal. The world is his oyster.
Now, everyone's "ohshit" and Sasuke and Naruto agree to put their differences aside to fight Orochimaru, knowing that he'd pretty much straight up kill them and then rule the world. Kakashi and Gai join in, along with the Kage's who arrive battered but still alive. Big fight begins and Orochimaru is growing increasing insane with power as he learns his new body and starts owning shit. Old Earth Kage guy gets batted around, Gaara holds on with sand defense and Water Kage, Ai and Tsuande can't seem to land a blow. Kakashi, Gai, Naruto and Sasuke combine to attack with some convoluted, multistep plan which looks like it works, but nope, fails. Probably because Orochimaru finds Susanoo. During this, Kakashi is injured in his non-sharingan eye, blinding that one. He has bad luck with eyes.
Orochimaru straight up kills one of the Kages... let's say Water, since, I dunno. Naruto goes all noble and tells everyone to stay out of it, no one needs be killed. Everyone's like fuck that, but Kakashi, tiring severely, tells them to trust him. Naruto steps out but Sasuke joins him because hey, this is what has happened since the beginning. Naruto is arrogant and Sasuke doesn't let him have the whole show. They fight, things are big and explosive but Orochimaru is getting better and of course, he's a edo as well, which sucks for them. Eventually, Orochimaru, who's using tonnes of jutsu's not just Sharingan/Rinnegan hax because he's awesome like that, finds the link between the eye powers and the Kyuubi and he latches on and yanks the Kyuubi out of Naruto, Sasuke is just too late to save him. Naruto holds on but is severely weakened.
Everyone rushes to his defense. Ai loses a leg but keeps fighting, Gaara's defense fails and is badly wounded, Gai goes Eight Gates, pushes Orochimaru back but can't kill him, but buys them enough time to save Naruto. Gai dies with a thumbs up. Tsunade releases all her chakra into Naruto telling him he must achieve his goal to be kage and gives her will of fire, and life, to him. Much tears.
Now, Sasuke is tiring, the kages are beaten and things look bad, but just as Orochimaru is about to crush them with METEORZ, Obito pops back up and warps it away. After this, Naruto has sucked up a shit load of natural energy and jumps back into the fight as Sage Master Naruto (let's give some bullshit reason that he's learned to draw Natural Energy while moving). During this fight, Obito is trying to help but is ineffective, he meets up with Kakashi, who's spent and near coma, they have a heart to heart about Rin and friendship and Kakashi reminds Obito who he was and gives his eye back. With both eyes, Obito gains new strength and is far better at his attacks and Kakashi is now completely blind but too weak to do anything.
Sasuke, Obito and Naruto fight Edo Madara Orochimaru + Kyuubi, more big booms and multiattacks. Obito manages to push the Kyuubi back into the Juubi trap he set up a long time ago, but is badly wounded in the process. Orochimaru calls him a loser Uchiha and kills hime. Sasuke is pushed over the edge and goes all bat shit on Orochimaru. Naruto uses this time to create a Spirit Bomb, er, super Rasengan? using all the Natural Energy he can, but doesn't know how he'll hit Orochimaru with it nor how they'll seal him. Sasuke is knocked away and Orochimaru see's what Naruto is doing and laughs at him because "durr hurr you won't hit me" But Kakashi, blind and weak, leaps behind him, arrogant stupid Orochimaru, and chidori's him through the chest and grabs hold telling Naruto to kill him. Naruto, crying like he does, complies and the massive rasengan shurikin thing obliterates Orochimaru.
But he's an edo and despite the deep destruction, starts to reform. The survivors are like, how we seal him. The mind reading guys with Shikamaru's dad tell them but they don't have enough Chakra. Naruto tries to get enough Natural Energy but it's not fast enough. Sasuke finally goes "we don't have enough but my eyes do" and he sacrifices the power of one of his eyes in once of those stupid reality bending things to seal Orochimaru away forever this time. But there's still the tailed beasts and both Naruto and Sasuke decide they too must be eliminated, but one eye isn't enough so Naruto gives his chakra to Sasuke to achieve this.
Orochimaru gone; tailed beasts gone; sharingan gone. All tied up and war is done. You can then do some flash forward chapter in which Naruto is hokage, Sasuke is some sort of blind ninja who is a bit of a pansy pacifist now because of all the evil he did and you can give fans all that love crap that really doesn't matter, like Naruto's banging Hinata now and she's all preggers with two kids already and Sakura is still pining for Sasuke who doesn't reciprocate even still. Manga done PLUS a potential for future generation crap if the greedy publishers aren't done.
tl;dr The key plotline is Orochimaru gains control of Madara and restores himself to the proper position as Big Bad in this manga.