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Okay these are a couple theories that I put together that aren't necessarily true. I just think that they would have been good plot twists.
Jiraiya and Hiruzen were in on it.
Okay as we know Hiruzen and Jiraiya chased Orochimaru out of the village some years ago. But let's look at what he did before that. He kidnapped a bunch of kids and tried to give them Hashiramas DNA so he could recreate Mokuton. What purpose would he have to recreate Mokuton? For the same reason he was obsessed with attaining the Sharingan. Those are the two best known ways to seal the Kyuubi. Other than RDS of course but as we all know Oro has done research into that as well. Why? Because he wants the Kyuubi? Doubt it. Because he wants to learn all the jutsu in the world? That's not a realistic goal and he knows that. So why would he put so much work into all this? Hiruzen wanted him to. Remember that Oro left right after he was successful. He claims he didn't know. I say the whole thing was a ruse. Hiruzen ordered the experiment and Orochimaru couldn't leave until he was successful. Then they put on a nice little show to throw off any Akatsuki spies. Yes that's right Orochimaru went to Akatsuki as a spy for Hiruzen. Afterwards he caught wind of the Uchiha massacre and that Sasuke was the only one left alive. That's when he turned on Hiruzen. He realized that the entire thing was a bid to ensure the Kyuubi stayed loyal to him instead of the village. In comes Itachi. One of two things happened here. Oro cut off communication with Hiruzen and when Itachi showed up Orochimaru figured it was only a matter of time until Itachi bumped him off. 2. He tried to take Itachis eyes so that when the time came he would be able control the Kyuubi as well. When that didn't work out he set his sights on Sasuke. He knew Hiruzen would get in the way so he decided that it was time to kill the old man. Otogakure was supposed to be a puppet government that Konoha could control and call on at a whim. Unfortunately Oro was in charge of setting up said government. With Otogakure at his back he still wasn't strong enough. He needed reinforcements. Who would be the weakest and easiest to take out? Suna. The Kazekage was a scumbag as well to boot. So he killed him and took over Suna. He attacks and kills Hiruzen the man now responsible for his exile. Then he tried to turn to the one person who could help him. Tsunade. He was hurt and she could heal him. Unfortunately Jiraiya came along. Jiraiya having been in on Oros fake betrayal but angry over Hiruzens death assumed that Oro had simply betrayed them. He attacked and Oros false reputation turned Tsunade against him in the end. Later he tried to take Sasukes body so that he could control the Kyuubi should Naruto ever lose control again. Then despite all his opportunities he never attacked Konoha again and has shown no desire to even now when it's most vulnerable. And now that Naruto has full control over the Kyuubi he has no need for the Sharingan because he isnt worried about it running wild. That's why he never attacked the village again nor has he tried to take out Sasuke with four kages under his control. He didn't hate Konoha. He hated Hiruzen. He doesn't want the Sharingan. He wanted to ensure the Kyuubi wouldn't go on a rampage across the countryside.
Sage you are...NOT the father!
Okay I came up with this idea watching CSI so bear with me. There is a real life disease called Chimerism. Basically you eat your twin in the womb and your bodies kinda meld. Its actually possible in some cases for you to sire or give birth to your siblings child instead of your own. My theory is this. The Elder Son is actually the child of the Juubi which is why the Elder son inherited the Juubis eyes while the Younger Son was the true offspring of the Sage. If the Uchiha descended from the Elder Son then it stands to reason that the Juubi is the cause of their oh how do I say this without pissing off the Uchiha fans "emotional and moral ambiguity." It also would explain the Uchihas ability to control bijuu beyond simple genjutsu. Its because they have a weaker version of the Juubis eyes and similar chakra.
All right have fun dissecting them.
Jiraiya and Hiruzen were in on it.
Okay as we know Hiruzen and Jiraiya chased Orochimaru out of the village some years ago. But let's look at what he did before that. He kidnapped a bunch of kids and tried to give them Hashiramas DNA so he could recreate Mokuton. What purpose would he have to recreate Mokuton? For the same reason he was obsessed with attaining the Sharingan. Those are the two best known ways to seal the Kyuubi. Other than RDS of course but as we all know Oro has done research into that as well. Why? Because he wants the Kyuubi? Doubt it. Because he wants to learn all the jutsu in the world? That's not a realistic goal and he knows that. So why would he put so much work into all this? Hiruzen wanted him to. Remember that Oro left right after he was successful. He claims he didn't know. I say the whole thing was a ruse. Hiruzen ordered the experiment and Orochimaru couldn't leave until he was successful. Then they put on a nice little show to throw off any Akatsuki spies. Yes that's right Orochimaru went to Akatsuki as a spy for Hiruzen. Afterwards he caught wind of the Uchiha massacre and that Sasuke was the only one left alive. That's when he turned on Hiruzen. He realized that the entire thing was a bid to ensure the Kyuubi stayed loyal to him instead of the village. In comes Itachi. One of two things happened here. Oro cut off communication with Hiruzen and when Itachi showed up Orochimaru figured it was only a matter of time until Itachi bumped him off. 2. He tried to take Itachis eyes so that when the time came he would be able control the Kyuubi as well. When that didn't work out he set his sights on Sasuke. He knew Hiruzen would get in the way so he decided that it was time to kill the old man. Otogakure was supposed to be a puppet government that Konoha could control and call on at a whim. Unfortunately Oro was in charge of setting up said government. With Otogakure at his back he still wasn't strong enough. He needed reinforcements. Who would be the weakest and easiest to take out? Suna. The Kazekage was a scumbag as well to boot. So he killed him and took over Suna. He attacks and kills Hiruzen the man now responsible for his exile. Then he tried to turn to the one person who could help him. Tsunade. He was hurt and she could heal him. Unfortunately Jiraiya came along. Jiraiya having been in on Oros fake betrayal but angry over Hiruzens death assumed that Oro had simply betrayed them. He attacked and Oros false reputation turned Tsunade against him in the end. Later he tried to take Sasukes body so that he could control the Kyuubi should Naruto ever lose control again. Then despite all his opportunities he never attacked Konoha again and has shown no desire to even now when it's most vulnerable. And now that Naruto has full control over the Kyuubi he has no need for the Sharingan because he isnt worried about it running wild. That's why he never attacked the village again nor has he tried to take out Sasuke with four kages under his control. He didn't hate Konoha. He hated Hiruzen. He doesn't want the Sharingan. He wanted to ensure the Kyuubi wouldn't go on a rampage across the countryside.
Sage you are...NOT the father!
Okay I came up with this idea watching CSI so bear with me. There is a real life disease called Chimerism. Basically you eat your twin in the womb and your bodies kinda meld. Its actually possible in some cases for you to sire or give birth to your siblings child instead of your own. My theory is this. The Elder Son is actually the child of the Juubi which is why the Elder son inherited the Juubis eyes while the Younger Son was the true offspring of the Sage. If the Uchiha descended from the Elder Son then it stands to reason that the Juubi is the cause of their oh how do I say this without pissing off the Uchiha fans "emotional and moral ambiguity." It also would explain the Uchihas ability to control bijuu beyond simple genjutsu. Its because they have a weaker version of the Juubis eyes and similar chakra.
All right have fun dissecting them.