Well, since there have been lots of things that ticked me the wrong way... lately... I'd do something like this...
As Naruto glares at Pain the earth begins shaking the wind blows really strong, thick black clouds cover the sky as rain begins falling heavily, fire erupts from the bottoms of the earth and there would be seen both life and death... in the depths of nothingness a voice whispers: "Now you've done it!" voice heard by every soul, alive or dead, a voice that brings fear on the face of Danzo: "This can't be true! I will not accept it!"
Tsunade smiles and falls to the ground: "We're saved!"
Everything becomes still as a cheerful laughter is heard approaching... closer and closer, bringing new life to nature. Suddenly Pain is thrown into darkness, thick, fearful darkness. "Playtime is over, thank you for taking care of my ne-phew!"
Naruto is stunned to see a dark haired girl, no older than him whisper at "Pain's" ear right before he falls to the ground unconscious.
The girl comes close to him, so close that he can see her up-side-down and stare right into her eyes: "So let's go to the village Naru-chan" .... "Who am I? That's what you are thinking, right? I am your dad's younger sister, Raisa. Now when his presence inside you has faded and since he is no longer alive, I have come to look after my cute nephew, no worries, I will tell you about your family, as much as you want.... and yes I am reading your mind... I can read people's hearts." Naruto stares at her stupidly as tears fall from his eyes, he too can read her heart, she was considered a monster as he was, he see it in her eyes, sad deep black eyes, dangerous eyes indeed, eyes with no warmth, no hopes, no life.
They enter the ruins of the village and face Danzo and his ANBU.
"Yo a$$hole, not dead yet? I bet you thought I was killed by the Third and Onii-chan. Too bad for you, I am alive, and have been for all this time, at the Center of the Earth" she then smiles while closing one eye, the next instant all the assassins behind Danzo fall to the ground, their bodies dried up.
"Aww... sorries, I love water so much, I had to get me some.... right from the bodies of your assassins." as she passes the frozen old man, followed by Naruto, one tear appears on her cheek.
Her body floats right above the village 6 men appear surrounding her in the sky, they have inscribed on their skin: "Water", "Air", "Earth", "Fire", "Life", "Death". All of them create jutsu's invisible to the human eye, as the village is brought back to it's original form and as all the ninja's have their wounds healed. Kakashi is unfortunately already dead.
The girl lands on the ground, then turning her head towards Naruto: "Come, let's talk to your dad for a bit".... "It's not impossible, have you not learned that nothing is impossible in the ninja world?"
They approach the graves of the late four Hokage. While Naruto keeps staring at Minato's grave, Raisa begins chanting and a frightening being appears, a death god with a knife in his mouth.
"Yo shinigami, wha'ssup?"
"I haven't seen you in a long time, your soul looks even tastier than 18 years ago when you first conjured me."
"Really? Well, I have been training it, just my soul, wandering around through the world, learning and growing it, it's like traning a pet."
"Haha~ You are so strange for a human, so what do you want this time?"
"This time I want the four most tasty souls you have taken from this village. I will use them all, and when they will be destroyed again, they will all return to you, with my soul as a bonus! How is that deal? I know you've waited a long time for it, and since you helped me before, why not as it from you and give what you want."
"Because I have the soul of your brother"
"True, indeed, I want The First, The Second, The Third and The Fourth Hokage, their souls will not break in this world, I bind them to mine, I make the choice freely and will abide by it until I decide is over."
"It is unlike any other trade I made, but it's fair, Done!"
The sould of the four great men appeared while the girl took out a knife and carved "Life" and "Death" on the palms of her hands, and uniting them, the bodies of the four crawled out of their graves and each called it's respective soul, thus the great men f the village lived again, in true body and soul.
"We will destroy all the enemies of Konoha. Besides your rightful abilities, you all control one element at your whim, just by thought. It's my present to you. Now it's time to leave. Naruto is coming with us."
So they all leave and start to kill, first all the remaining Akatsuki members, except Madara, then as they get closer to him, Naruto is taught how to control the fox, being able to unleash and seal it at will. He makes a deep bond with Minami, learns what happened to his mom, who had to leave him and the village in order to protect him from everyone knowing that he was The Fourth's son and where to find her. They all find Madara who is god-like, fighting back against all their jutsu's, who also unleashes the other half of the Kiyuubi, killing, almost, all the other former hokage. But is eventually killed by Naruto who as well as Sasuke is immune to Madara's MS tricks, due to Itachi's help.
Naturo returns to the village carrying all the bodies, Raisa's close to death as all her energy would have been drained due to the fight, while she had kept, "Life" and "death" unleashed. She now gives them to Naruto who is attacked by Sucks-ke, who thinks that by killing Naruto, who would be, logically, the next hokage, will have his revenge on the village... and who(Naruto) unknowingly uses "Death" against Sucks-ke, thus killing him, now Naruto has to chose from keeping his aunt alive and from bringing back his traitor friend, he chooses as Jiraiya chose long before, to forget about his friend and so Naruto uses "Life" and brings back his aunt, thus keeping his dad alive as well...
"And they all live happily ever after" until Raisa decides to fulfill her part of the bargain with the Shinigami, not before spending lots of precious time with her family.
The End!
Sorry got a little carried away... >_>