Note: This is mostly a text version of chapters 508-512. So of course I don't own any of this. As you might imagine this contains massive manga spoilers that are not yet out in anime form as of writing this. The Naruto portions were added by me as I feel this is how it SHOULD have happened.
Chapter 1: The Flower of Hope
It was nicknamed the "Land of Rain" for a reason, it poured every day for as long as anyone could remember. Perhaps the land was cursed, their geographical location always caused them to be in the middle of other nations wars. Whatever the reason, the water would run red with blood as it often does. Two cloaked figures faced off, a battle that was destined to happen. She was the Angel of the village, the right hand person of the former leader. And he was the man who declared war on the world, his goal of world domination was in sight. She knew this day would come. She had carefully planned how to defeat him, this was the moment she was waiting for. There was no fear in her eyes, if she failed all would be lost.
Instead of heading right into battle, he folded his arms and began to speak. "Let me ask you one thing, why did you betray me?" She gave no response. "Is Naruto Uzumaki really worth all that?"
She raised her arm and pointed at him. "He is the Light. That's why we all have the flower of hope." With that she began to break her body down into sheets of paper.
He simply giggled at her statement, not taking her seriously at all. "You bare your fangs at me yet you still wear that uniform. I can only assume you still have some lingering affection for Akatsuki."
At this point her body was completely made out of paper. "Yahiko created Akatsuki, the red cloud is a symbol of the blood that fell over Amegakure during the wars. You may have taken over Akatsuki, but this uniform is ours, not yours. The Amegakure ninja Nagato was the one who awakened the Rinnegan. It is not yours, either. His eyes are this Country's...this Village's treasure." She tossed a number of paper shurikens at him.
He stood there as the projectiles passed through his body. "You are mistaken about two things, but since you are about to die I will enlighten you. I am the one who induced Yahiko to form Akatsuki and I am the one who gave Nagato the Rinnegan. So I guess you could say I am here to take it back." Her face was a mix of shock and confusion. "But it doesn't matter. From where I stand, you are an ignorant little girl. However, you are a little girl who knows where Nagato's Rinnegan is. All I need to do is capture you, don't underestimate the power of the Uchiha eyes."
She formed her paper wings and took to the sky. Strategically, she positioned paper all around his ethereal form waiting to attack. He began to use his eye power that enabled him to suck solid objects into his own dimension. Little did he know that the papers were changing. "I slipped in some paper bombs, I will take you with me into the next world."
Meanwhile Naruto was chasing a shark who had a scroll in its mouth. He was in his new, improved Sage Mode. But even with this speed boost, it was only just enough to keep up with the shark. "If I can't catch it, I will just destroy it when it reaches its destination." Naruto had little idea how fast and far he had traveled. In a way it was as if instinct alone had taken over.
Madara was a mess, his right arm was blown off and his mask was partially destroyed. "I guess I underestimated you. But come to think of it, you are a former Akatsuki member after all. It seemed you were planning to explode the moment I swallowed you. You intended to take me with you and you failed." She was breathing heavy, her assault cost her a great deal of Chakra. "I was too quick for you and swallowed most of the explosion, though you did manage to injure me... but thanks to me, you're still alive. You should be grateful, but I have to ask: is this the extent of your secret plan?"
Konan didn't answer his question, instead she asked one of her own: "Why do you think we betrayed you?"
He casually shrugged it off. "Who knows, that's your problem."
A gigantic paper trench parted the sea around them. "It's because you are the darkness. Flowers can only wither in a world without light." She attached a number of paper bombs to his body, denying him the ability to teleport.
Due to the mask it was difficult to read his expressions, but that lone eye was visible and his anger was clear. "You almost had me there. I'm surrounded by explosive tags that could go off at any moment, I can't afford to be careless."
She had the same expression of anger on her face, at last it was just about over. "And you can only slip through physical objects for five minutes." She had figured out his powers and knew exactly how to exploit them. "I prepared six hundred billion exploding tags to kill you. They can explode continuously for ten minutes." She then began her chain reaction for ten minutes and at the end, fell to her knees panting. "Madara, he has to be..."
He appeared right behind her unharmed and with his arm back, it was over. "Dead?"
She was too exhausted to fight anymore, she stood up with a blade to her back. "How? You had to have died. I ran simulations over and over, this should have been enough to kill you."
He spoke calmly as his victory was assured. "Izanagi. It is a forbidden Uchiha Jutsu. You lose the Light, but you gain the ability to connect illusion and reality. It's only available to those with the power of both Senju and Uchiha." He drove his blade into her back causing her to cough up blood. "The world thinks Madara Uchiha lost to Hashirama Senju, but what is the reality? He who sees the future is the victor, the true battle has yet to come. Our previous battle was just so I could gain his power. I am Madara Uchiha with the power of Hashirama Senju. I am the only one who can be the second Sage of the Six Paths. Looks like you will be reunited with Nagato soon. There the two of you can share your regret for falling for Naruto's nonsense."
Madara's overconfidence got the better of him as a Rasenshuriken spiraled into his back. A clone of Naruto pulled Konan away from the blast at high speed. Izanagi could not be activated possibly due to the speed at which his body was breaking down and the pain it caused. His midsection was completely disintegrated and his legs were being swallowed up as well. Before he was completely consumed, he smirked and said: "The peace you seek is nothing but a fools dream, there will always be somebody like me."
Before turning his attention to Konan, Naruto smiled at what was left of Madara and stated: "And there will always be somebody like me to stop them."
Note (again): I have yet to decide if this will be a one shot type of deal or a long term story. Konan is the best character in the entire series btw.