This is just what I imagine the ending would be like.
Everyone has their own opinions so I felt like writing down my own imaginative ending of the Shippuden story =].
Feel free to R&R.
As the battle between Uchiha Sasuke and Uzumaki Naruto raged on, the village quaked as blows were negated. The people hid in shelters underground as Uchiha Madara watched from the Hokage Monument. Tired of the endless battle, Sasuke activated his devastating ability, the Mangekyou Sharingan, staring deep into Naruto's eyes and trapping him in a Genjutsu. As he did, the genjutsu was suddenly turned against sasuke himself, believed the only person was the power of his older brother.
"Wh-where am I?" he mutters, looking around the place to only see a vast open area of bright light.
"Sasuke..." A voice called out. Sasuke traced the voice back to what seemed to be an image of his older brother, "Naruto isn't your enemy... neither is Konoha"
"What are you talking about?!" he yells, "I know what Konoha has done to us... to the Uchiha Clan" he begins to tense his gaze.
"Are you sure you know, or do you know what Madara has told you?" he asks his little brother, "It's true that I slaughtered our clan for the peace of Konoha... but believe me when I say that I wasn't going crazy that day when the clansmen came because they were suspicious of me. If you know everything I know, then you know that the Uchiha Clan would kill anyone to be supreme. Friends... Family... none of that matters because the Clan will do everything to gain power."
Sasuke stood there motionless, remembering the words Itachi spoke to him all those years ago. That to obtain the Mangekyou Sharingan one must sever the bond with someone they are close to. "Friends..." he says in a low voice. He then remembers what he said about the Eternal Mangekyou Sharingan, obtained by taking the eyes of one's own sibling, "Family..." he lowly says.
"See... I died... so you would rebuild the clan in eyes of love and care. To gain power without killing those close to us" Itachi calmly states, "You cried when I killed everyone... and when I died... you alone is capable enough of rebuilding the clan. Goodbye..." With that, Sasuke was released from the Genjutsu, his gaze focused upon the man standing on the Monument.
"Karin, get over here" Sasuke ordered as a girl with long red hair landed next to him.
"What is it Sasuke?" she asked him.
"Open your arm out, and you Naruto... get up before I change my mind." He ordered the both of them.
"S-sure." Naruto hesitantly responded, getting up. "What do you want...?"
Karin opened her arm out as Sasuke took a bite, restoring his Chakra. He looked over at Naruto will his Sharingan de-activated, "We need everyone aiming at that man over the monument, so get into your Sage mode now. Karin, because he can teleport and appear anywhere at will I want you to stay with the 5 kage's."
Karin nodded and ran towards the group of Kage's who were standing on the top of the Hokage's building as Naruto calmly sat on the ground crosslegged in order to build up his lost Sage chakra. "Just what are you planning Sasuke" Madara said to himself as he gazed at Sasuke, as he looked at the masked man with his Sharingan. Before he could react, Madara appeared in front of Sasuke in an instant, kneeing him in the stomach. Quickly, Sasuke put Madara into a lock and proceeded to release his lighting chakra in the manner of his Chidori stream.
"I'll buy you some time!" Sasuke yelled over at Naruto who was still gathering Sage Chakra. Madara tossed Sasuke aside and proceeded to attack Naruto until a large arrow seemingly pierced Madara from behind. As he turned around he witnesses Sasuke's Susanoo activated fully. He forces the arrow out and flings it back at Sasuke who blocked it with Susanoo's Sheild/crossbow.
"Hurry up Naruto!" He yells as he had Susanoo grab Madara in a tight grip, "I can't keep this up forever!" feeling the pain in his cells grow as Madara continues to resist being gripped tight.
"This jutsu is mere pre-school compared to my abilities" Madara states as he breaks through Susanoo's hand. Sasuke falls to the ground as he feels the pain aching horribly in each of his cells as loud shrieks are heard. He is then surrounded by a thick ray of light as he sees Itachi holding his hand out with a smile on his face. Sasuke took his hand and stood up, feeling greater power, feeling Itachi's spirit living on with him, gazing at Madara with his Eternal Mangekyou Sharingan.
"This is for you brother..." Sasuke said as he summoned Susanoo, clad in armor resembling a mix between Itachi's and Sasuke's. The warrior grabbed Madara with both hands, glaring at him with eyes resembling Sasuke's EMS. "Now burn..." Sasuke mutters before an eruption of black flames engulfed Madara. Just then Naruto is seen creating a wind rasenshuriken with both sage and the ninetails chakra. Sasuke jumped away from the area, as Naruto slammed the newly formed Rasenshuriken into Madara, destroying not only his eyes, but his entire body as well.
As the dust cleared, nothing was left but Uzumaki Naruto who stood before a giant crater in the ground. Sasuke appeared ontop of the Monument, and grinned to himself, acknowledging Naruto's growth. He looked next to him to find Karin standing. "Karin... I apologize for impaling you when we were up against Danzou, but you know what my goal was."
"I know... it was also my doing for letting him use me as a shield" She replied, her obsession with Sasuke turning into sincere affection.
"Where Orochimaru created the land of sound... that will be my new home... where I will rebuild the Uchiha Clan the way my brother would have wanted it" He said sheathing his blade, "Because of my actions the Uchiha are officially extinct in the area of the Land of fire". He jumped to the ground, walking past Naruto before stopping, "You are indeed a worthy rival... and friend".
"Same goes to you too... Sasuke" Naruto replied. Sasuke made his way out of Konoha's gate along with Karin who tagged along behind him.
As the two made their way into the distant horizon, a ghostly image of Sasuke's family gazed at their son with a smile on their faces.