Framed
Somewhere in the middle of the night, Naruto was pulled away from his bed and hull before the council in session. The Hokage wanted to help him but the crime in question was simply just too severe that he couldn't take it lightly. According to the witnesses, several civilians saw him exiting from the Uchiha's place before returning to his own home. They claimed the boy was up to no good thus as good citizens they followed him.
Unfortunately, when they have gotten a better look they were horrified to see he's covered in blood. So after reporting to some Chunins, they searched his house and found his bloody jump-suit along with his bloodied shoes. At least that was the evidence they brought to light when the trial got started.
Sadly from Naruto's testament, he said he knew none of the said evidences. He claimed he had only went to the Ramen stand then back to his house before being dragged to this meeting. Obviously, his testament was not very convincing. Especially when it was paired against the so-called 'evidence'.
It seems somewhen after the massacre, a group got together and started a conspiracy act against the boy. They managed to procure his old and unwashed clothes dropping them in pools of blood before hiding them in his room. The same with his shoes as they create foot steps of a child exiting from the dead clan. Since most of the ninjas were busy looking for the killer and securing the village, no-one witnessed their strange actions.
The civilian council too acted as they plant false witnesses for their grand scheme in order to get rid of the demon. The Hokage knew they had been trying to get rid of Naruto for a while but didn't know they would take opportunities in times of village crisis. He had truly underestimated them thus how Naruto is ended up paying for the price. Sadly their so called evidence were air tight thanks to all the chaos generated by the massacre.
"Hokage-sama, with all due respect. You are obviously clouded by your personal feelings for the boy to not see the evidences presented before you."
With that one line, the councilor gain some of the Hokage's supporters. While not voicing out loud, they too starts to see their leader acting in the interest for the boy. It was clear that the Hokage had a soft spot for him but with the accusation rising against the kid, they needed a leader with more objective thinking.
The councilor knew he's getting an upper-hand because the whole knew their leader gave the boy a lot of lean way. He was even allowed to call him with dis-respectable names. Bringing the matter back, the councilor pushes forth with his attack.
"We had several key witnesses seeing him exiting from the crime scene."
The Hokage knew he had to respond quickly and with a more neutral reaction if he wants to convince others of his leadership ability.
"Councilor, that's quite a wide accusation. Do you think those witnesses are willing to subject themselves to a mind walk by an Yamanaka?"
"Perhaps, Hokage-sama."
They couldn't outright reject the mind walk because it would made it seem like they were guilty themselves.
Despite that, the civilian council had everything planned. Since they had mind-walking clan, it's not unreasonable to assume an Yamanaka would be asked to verify their claim. However, the tricky part is to get the right Yamanaka to do the mind-walk. They may not be able to get to the head Yamanaka (Inoichi Yamanaka) but if they can sway the next best it would be enough.
Thanks to the village's unfair prejudice against one boy, it wasn't difficult to find one willing to submit to their clause. They knew if they ended up with a mind-walk, the likely candidate would be Inoichi. Hence, all they need is to ensure another Yamanaka takes his place. As long as the Yamanaka in question is one of Inoichi's trusted clan member, it wouldn't be difficult to switch them.
Then again, it turns out it wasn't needed as the councilor pressed on.
"However, considering the bloodied clothes found by your shinobi. I don't think it would be necessary."
"Hokage-sama, even after this. Can you still say the child being innocent?"
It was a two point attack, one with hard evidence and the other targeting the leader's obvious deliberate attempt to protect the child."
"Councilor, I would watch your tone and accusation."
Even the benevolent leader couldn't help but get a little angry.
"In Konoha, everyone is 'innocent' until they are proven guilty."
"This is especially the case when that someone accused is anything but a child."
Unfortunately, his word of wisdom fell on deaf ears as the civilian side of the council rolled their eyes. They had longed learned to hide those little dis-respective actions in council meetings. It's their little rebellion as they test the boundaries to how much and far they can get away with their actions.
Anyway, as the council turns to the 'evidence' they all recognized the boy's clothes. Only he wears the color of orange hence it's no mistake they were his clothes. If that's not bad enough, they were still covered with their village founder's blood, thus making his case more tricky than it already is. Even without voting, the council in session could sense where the verdict is shifting.
Combined with several 'key' witnesses' testament, things aren't looking good for our Jinchuriki.
"I did councilor, I saw the de.. boy leaving the Uchiha district."
"I can recognize his bright orange jump-suit anywhere."
The councilor didn't need to verify the bloodied clothes as evidence.
Similarly, other witnesses says same things, all incriminating the boy.
"At first, I didn't who it was. He looked fishy so I came closer for a look."
"Then, I knew who it was. Only he wears that stupid color."
"I was going to teach him a lesson until I saw the bloody clothes, so I called the Anbu."
The Hokage tries to pick out the inconsistencies but they were all solid.
"Hokage-sama, I would recognize the de... the boy anywhere."
"Aside from his ridiculous color, he's the only one in the village with whiskers."
Again, the leader tries to point out it could be other shinobi henging.
"Hokage-sama, why would anyone henge into the boy?"
The Hokage wanted to say his own shinobis but he had to reminded himself for not throwing wild accusation. So until he had prove, there's very little he can do. He had vowed to form an investigation team after delaying the sentence but things aren't going his way.
The Hokage may know the truth that it's Itachi's secret mission, but it wouldn't prove Naruto's innocence because they could had done it simultaneously. Sasuke was no help neither since he's in a coma. Unfortunately, some of the shinobi clans too starts to suspect Naruto.
Thankfully, some of the more open minded raised a valid point.
"Councilor, how do you explain a child kill the so-called elites of Konoha?"
For once, Shikaku Nara wasn't asleep as he brought up one major contradiction.
Unfortunately, the councilor was confident.
"Excellent question, Nara-dono."
"As much as I hate to admit, the boy was an abnormality."
"I am sure the council is familiar how he had an uncanny ability to outrun ninjas."
"Even his pranks were something no normal could ever thought of, thus catching Chunins and Jonins alike."
"Lastly and most important of all, we all know what's reside within him."
The councilor wanted to call him a demon but used the term the Hokage used. Despite Shikaku raising a reasonable point, the doubt was quickly clenched by the councilor's casual explanation.
He didn't need to say the Kyubi as the whole council knew what he's referring to. While common sense dictates that the demon's chakra was never used, the shinobis were afraid. Hence, in this scenario they would rather Kyubi not being among them then the possibility it would one day go berserk. The damage was already done as even Shinobi clans starts to nod to the councilor's words.
He was also right in his pranks as he does have quite a knack in trap making. Sadly they were just too creative and ingenious thus catching even some of the Anbu off guard. Unfortunately, those facts while useful as ninja candidate it doesn't help his case. In fact they were counter productive as the councilor points out how a more lethal version could be used to kill even the elites of the village.
It was for this reason more clan members starting to favor the councilor. With so many hard evidence against one boy, the Sandaime's in a difficult situation. If that's not bad enough, news of Naruto's involvement in the Uchihas massacre was somehow leaked. As the rumor spread across the village, protesters had gather outside. It was obvious what they want as they all were calling for the demon's death.
Even if by some miracle they somehow managed to win the case, the village is now too dangerous for him. As far as the civilian's concerned, Naruto 'IS' the only one responsible for the massacre. Even the real culprit is caught, in their minds they already concluded that the demon is in fact the master mind. Hence, it's quite impossible to reason with them.
Despite his shame and anger, the Hokage managed to take 'Public Execution' off the table. However, life imprisonment sentence isn't anywhere better. It took a while to convince them as the council all demanded for true justice as did the public outside.
The people were now more angry than it was just the Kyubi incident. Years in waiting and watching, he finally show them his demon side. Sadly, it was already too late as the demon took away their greatest clan's lives. They didn't want just his blood but also the years of torment they had to endure from his presence.
For this reason, the Sandaime had no choice but to quickly send him away. It may be a prison but it will safer than Konoha. As for the civilian council their only consolation was they were finally able to get rid the demon boy.
Whether Naruto's guilty or not, it didn't matter as the people were too irrational to care. The death of a whole clan but one is just too much for them, especially where it involves the founders of their village. Once they hear the rumor that the demon child may or may not be involved, it triggered an instant chain reaction as everyone vote for his death. They tolerate him all these years because he had yet to show his colors. Now that the village's greatest clan was dead because of him, his life is as good as forfeit.
Imprisonment
When Naruto first heard he's going to prison he's deathly afraid because he will be surrounded by criminals and killers. However the Hokage reassure him, letting him know it's only temporary. He claims that the village is just too dangerous for him now, hence he's better off insider the prison. It maybe a place full of criminals but he will at least be watched by the guards.
The Hokage says they were no different than the Anbus in Konoha. Despite his young age, Naruto's not ignorant. He knew people in the village dislike him, he just didn't know why. Then again the protesters outside weren't making it very subtle as they scream loudly for his head and death.
He thought he had seen them at their worst but he was wrong as the people were totally furious. Through the windows he can see the Anbus holding back the horde as look like they want to take a bite out of him. Luckily non look up to see him otherwise not even Gai could hold them back from tearing through the Kage building.
Seeing this the Sandaime urged his Anbus to hurry. So under their full protection, the young Jinchuriki was escorted away silently and safely out of Konoha. They had to take the roof tops thus avoiding the masses of the crowd. Even then they couldn't have done it without the Hokage as he mis-direct them by drawing their attention to their verdict.
Naruto could hear the roar, obviously from the reaction. It was difficult to deduce whether it was disapproval or an actual cheer because he was already at the gate. The Hokage did promise him once he fixes things, he could return.
Sadly to both parties, his return wouldn't be happening anytime as evidence of his innocence will be long gone. Unfortunately, since he's convicted as a criminal he will be serving his crime. On top of that, the nature of his crime is against the royal founder of the village and strongest clan he will be there for a very long time and most likely for the rest of his life.
The Sandaime can investigate as much as he can but with full hate of the population baring down on the poor boy there's very little he could do to prove his innocence. Every evidence will either be inconclusive or insufficient as the village as a whole work together in the background to made sure the demon boy can never set foot back in their village ever again.
After a while, the Hokage will eventually realize just how futile it will be. It will be like working on an up hill battle and against all the people he's swore to protect. Either way it will be tough and next to impossible to win situation.
As for Naruto, he was haul out of Konoha in chains quickly and silently away from any of the angry villagers. There's a carriage waiting for them as the Anbus escort him all the way along with the necessary documents. They had to take to the roofs to avoid the villagers as everyone was desperate to give the boy his last send off.
Luckily no-one saw them and the short trip was off to a quiet start. His guards sympathize his feelings, it's bad enough he's convicted as a criminal. The most they could do is to prevent the whole village from making it worst then it already is.
On their way Naruto said nothing and his guards were glad to leave him in peace. Those waiting inside the carriage had been expecting a missing-nin, but certainly not a 6 year old child. However, the furious reaction from the population shocked them as they hurriedly fled from Konoha.
They can still hear the shouts, had it not been the Anbus hurrying them along they would still be stunned. Deep down they knew whatever crime the kid had done no way deserved a maximum prison sentence.
Once they reached the Fire prison, the Anbus has to leave. There's little to be said, as there's nothing they could say to make things better. Then again, they doubt the kid had yet to see the reality of his situation. The most they could do was to give him a light squeeze on the shoulder before leaving.