Authors Note: Damn power outage just as I decide to start writing this chapter. For those that are curious about why no one realized Ino had been at the scene, I updated the previous chapter to take care of that. Looks like I will be doing shorter chapters and more frequent updates, at least for the time being.

OoO

Kakashi had given Ibiki the slip by creating a shadow clone in the bathroom and returned to the scene with Pakkun. "So what can you tell me Pakkun? I feel like there is something we're missing." 'Naruto's impulsive, but something like this, there has to be a reason.'

"Hmm I smell four people, but something's off." Said the small pug, sniffing around the alley, then moving towards the entrance. "I think one of them was a girl, smells like flowers. And I'm guessing the ramen scent is your student. In the alley the girl's scent seems much weaker, but it's there." he said motioning to the center of where the large drying blood pool was. "Then I get her scent on the wall here, and a slight hint of bile, but no physical evidence. Likely no one other than us hound summons, or the Inuzuka clan would even suspect there had been someone else here. So someone was here first and destroyed what evidence there was of the girl, and the thing that's bugging me, I can't smell them. I've eliminated, yours, Ibiki's, the ANBU who discovered the scene, the medic, and the Suna ninja, so either the person was able to mask his scent somehow, or the ANBU had something to do with it."

After hearing Pakkun's analysis he came to the same conclusion as well. "Yes I agree. Unfortunately, I'm not aware who that was and even if I did we don't have any sort of proof. So someone wanted this to look like Naruto senselessly murdered two ninja, twice his age. If that's the case, whoever the girl is, is in danger being the only other person apart from Naruto who knows the truth. Can you find out which way she went? We need to get to her first, and fast."

"No problem, seems she and Naruto left together. This way." Pakkun said jumping to the roof.

'This is the direction Naruto's apartment is in.' Kakashi thought to himself as he and the ninja hound jumped from roof to roof.

OoO

Ino stepped out of the shower and after drying off, redressed in her purple pajamas with flower print. She hadn't realized just how bad she looked until she stood in front of Naruto's mirror. She looked like she had waded waist deep in blood. Somehow she still didn't feel clean, but it was nice to be in clean clothes. She left her ruined outfit in the corner and decided she would throw them away or ask Naruto to do it. She stepped back into the room to see Naruto still there sitting on a blanket under the window.

He had been trying, since Ino went into the shower, to get the Nine-tails to talk but with no success. He'd asked about why it had gotten so upset at the alley, not that he hadn't been, but it seemed strange that a demon fox would care. After a while when he hadn't gotten an answer, he resorted to taunting it into talking, but that also hadn't seemed to rouse it. Once he had finished replacing the dirty sheets with clean ones, he gave up trying to communicate with the stubborn fox. "You can have the bed. Don't worry I changed the sheets." Naruto said. Ino nodded and resumed her place and position on the bed.

"Thanks again Naruto." Ino didn't feel much like sleeping though, she could still picture the men from the alley and feel their touch on her skin. "Can I ask you for a favor?" She was trying to hold back from crying again.

"Yeah, of course." Naruto could hear the strain in her voice even though he couldn't make out her expression in the dark.

"Please don't tell anyone what happened." Ino wasn't sure if she could deal with people pitying her. The memories of the incident were crushing by themselves, she didn't want to see the look of pity in the eyes of those around her on top of it.

"If you're sure." He waited as Ino nodded in consent. "Ok, I promise I won't tell anyone." He didn't know yet what he'd tell someone if they asked, but he'd figure something out, for Ino's sake.

Ino fell to her side, facing away from the window, keeping her knees to her chest and began to sob quietly. She made a vow to herself as tears trickled down her face into the sheets. 'I swear I'll become strong.' For once she did not think of Sasuke, but of herself and all her friends, including her new friend, the dead last from her class.

Naruto sat patiently as Ino's sobs stilled after a few minutes. He was about to ask if she'd like a glass of water, when a knock at the side of his window caused them both to jump. Naruto immediately stood up facing the window, while Ino sat back up maintaining her curled position. Just outside the window stood a man in black ANBU ops gear complete with a bird mask.

"Sorry to startle you. You're Naruto Uzumaki I presume?" the man asked staying outside the room.

Ino could feel her heart racing when the man spoke, even though he didn't seem aggressive. She started taking deep quiet breaths in an attempt to calm down.

"Yeah that's me, yaknow." Naruto replied, not dropping his guard. "What do you want?" he asked, giving the man a close look to make sure he wasn't reaching for any weapons.

"I'm here on orders from Lord Third. I have to take you in." Foo stated calmly. He didn't want to anger the boy in case he was volatile, though at the moment he seemed in control. He also noticed that a girl was in his room, he recognized her as Ino Yamanaka, daughter of Inoichi, his cousin. Torune decided not to comment on it, as the situation seemed innocent enough, with Naruto sitting on the floor with a makeshift bed.

"What does old man Hokage want with me?" Naruto asked still keeping a close eye on the ANBU.

"He just wants to talk with you about what happened with the Suna ninja tonight. It's important that you come with me now, or I will have to take you in by force." There was a stern edge to his voice, but he still made no move towards them.

"Aww damn it...fine" He looked back at Ino, whose expression was mortified in the moonlight.

Ino had wanted to jump up and grab Naruto's arm to keep him from going but she didn't want to get any closer to the man outside the window, she still hadn't calmed down. "Please don't...you promised." Ino pleaded, holding back the tears that threatened to fall once more.

Naruto shut his eyes in thought for a moment, then had an idea. "Ah, here. Shadow Clone Jutsu." Another Naruto appeared in the room and took a seat in the spot the original Naruto had been sitting. "Is this ok, Ino? I wouldn't go if I didn't have to, and you should stay here and get some sleep."

Ino calmed down a bit, avoiding hysterics, and nodded. As long as she didn't have to be alone, it didn't matter if it was just a clone. Naruto smiled at her as he stepped outside the window.

"Don't worry I'll see what the geezer wants and come right back." He then vanished from her sight following the ANBU.

Ino looked at clone Naruto once the original was gone. He gave her a small smile and said, "Don't worry I'll stay here till the real me gets back."

"Thanks." Ino replied finally starting to feel her heart rate returning to normal. "Is it strange to think of yourself as not real?" She asked, a little curious what would happen if she hit him with her Mind Transfer Jutsu.

"Hmm I don't know, never really thought about it, yaknow. I guess you could say I don't really feel like I'm not the real Naruto, but I know I'm not." He said while scratching his head in contemplation. "Ugh just thinking about it is giving me a headache." He laughed and smiled sheepishly.

Ino giggled a little. He certainly seemed like the genuine article with that idiotic grin on his face.

OoO

Pakkun stopped once he got close to their destination. "Kakashi, we've got a problem, the ANBU from the alley was already here. Smells like Naruto went with him, in the direction of the tower, but I think the girl is still here." said the dog, while sniffing at the air. "I'd say we missed them by about five to ten minutes."

"Damn it. Well first things first I need to get the girl somewhere safe and then I'll search for Naruto. Something is happening and I don't like it." replied Kakashi. For the first time in a while he was getting mad, someone was trying to cause trouble for his student and his village, and he was going to put a stop to it.

"Alright, well you're on your own from here Kakashi, my time is up. Later." said Pakkun, raising a paw in farewell and vanishing in a puff of smoke.

Kakashi stayed hidden while doing a quick sweep of the area to make sure there was no one else around and, then slowly made his way towards Naruto's apartment. He saw that the window was open so he approached there and listened, hearing nothing, he peeked inside. He could see Naruto sitting just beneath the opening on a blanket, 'Must be a clone.' and the Yamanaka girl from Asuma's team sitting on the bed in a somewhat defensive position. He now could imagine what had happened in the alley, and there certainly was no reason to fault Naruto for his actions.

Kakashi cleared his throat quietly to get their attention. The noise still surprised Ino, but the Naruto clone recognized the sound and got up and faced his teacher. "Hey Kakashi sensei. What's going on?"

"I'm not sure, maybe you should tell me. I saw what happened in the alley, care to tell me about that?" asked Kakashi with a questioning look.

"Ah that." Naruto's clone scratched his head, he didn't need to look at Ino to know she didn't want him to say. "It doesn't matter, I did what I had to do, and I don't regret it." He said with a determined look.

Kakashi took his eye off his student for a second to glance at Ino, she had relaxed a bit in her position at hearing that and he could hear a very quiet sigh. "Ok well I guess I will leave it at that for now." He replied returning his gaze to Naruto. "However I need to get you guys out of here, or I suppose I should say, I need to get you out of here Ino, since you're just a clone of Naruto."

"What, why?" Said Ino. She had been startled by Kakashi's appearance but she had been a little calmer than she had been when the ANBU showed up. Her heartbeat had increased a little though since his arrival.

"I'll be brief, I think Naruto is being framed for murder. I'm not sure why just yet, but you are the only other person who knows what happened, and I think that whoever is doing this, is going to come after you next to keep you from telling people the truth. Speaking of, do you know where Naruto went?"

Ino shook her head. "The ANBU just said that the Hokage needed to talk to him, and they left." she replied.

"Yeah, that's right, yaknow. They left a couple minutes before you showed up. He was wearing a bird mask."

'Hmm that's not a lot to go on, but it's something.' "Come with me you two." it wasn't necessary to bring the Naruto clone, but he figured that he was here to keep Ino calm or maybe just for company.

Ino hesitated for a moment till Naruto's clone turned towards, "It's ok Ino, we can trust Kakashi." She then got of the bed and left out the window after Naruto's clone.

OoO

Foo brought Naruto to the Hokage tower, but instead of taking him upstairs, he lead Naruto into the basement where the holding cells were placed. "Where are we going, I thought the old man wanted to talk to me." Naruto stated walking behind Fu, with his hands behind his head.

"Sorry Naruto, but you'll have to wait for Lord Hokage down here. Just a safety precaution, seeing as you did kill two ninja from another land." replied Fu, opening a cell door for him.

"Tch." 'They deserved it...they deserved worse.' Naruto thought to himself deciding it better to keep his mouth shut for now. He stepped inside the cell and took a seat on the wall-bed that was the only thing in there.

"Please wait here and I will retrieve the Hokage." said the ANBU and he retreated up the stairs. As Foo reached the first floor a voice spoke from behind him.

"'War is the truth of shinobi.'"

Foo stood still for a moment as the seal on his memories was released, then turned and knelt before his true leader. "Naruto is waiting in cell 1. I located the girl, she was at Naruto's apartment."

"Very good Foo, I appreciate your diligence. Before you take care of the girl, tell Hiruzen that Naruto is here twenty minutes from now. By then it will be too late for him to react even if he feels the Nine-tails chakra. I've already taken care of the night guard and sealed his body for the time being, to make it look like he was killed by the boy. In the confusion go take care of the girl. I know making it look like suicide should be no problem with your talents in the Yamanaka clan ninjutsu." Said the shrewd man. His plan was going perfectly. And with the entrance to ROOT on the same level as the holding cells, it would be no stretch of the imagination that he could be the first to arrive on the scene of a Biju rampaging. "I will be leaving your memory unsealed until you've finished your mission."

"Yes Lord Danzo." Then Foo vanished.

'Soon this village will be filled with true shinobi. I will make Konoha strong.' Danzo thought to himself as retreated back down the stairs.

OoO

Naruto got impatient with sitting after thirty seconds and was practicing his chakra control by walking on the walls and ceiling of his cell. Five minutes after the ANBU left, Naruto could hear foot steps approaching. "Wow that was fast old man." he said as he jump down from the ceiling. He looked out of his cell, but the man walking towards him was NOT the Hokage. It was a man about the same age, short black hair, bandages around his head, a cross shaped scar on his chin, and an outfit that concealed the right side of his body.

"So you're the sorry excuse of a Jinchuriki that the Nine-tails has the misfortune of inhabiting." Said Danzo looking down at the unimpressive boy. He was an example of everything he thought Konoha needed to be rid of.

Naruto could feel his anger rising, he wasn't sure what Jinchuriki meant, but the rest of what he said and the way he said it, was clearly an insult. "Who the hell are you gramps?"

"It's of no consequence to you. It seems like the only thing you inherited from your father was his looks." He said while unwrapping the bandages around his head and right eye.

"You knew my father?" asked Naruto, anger replaced by surprise. Naruto had asked the old man who his parent's were when he was younger, but he had just said that he would tell Naruto when he was older.

"Hnn I make it my personal business to know all the shinobi of this village, you included. Since I will be taking the Nine-tails from you, I see no reason not to enlighten you of your paternity before you die. You are the son of Minato Namikaze, the Fourth Hokage." Danzo stated, before ensnaring the young Genin in a genjutsu with the Sharingan he took from Shisui Uchiha.

Shin appeared next to Danzo as he finished placing Naruto into a genjutsu. "Be prepared Shin, this shouldn't take long."

"Yes Danzo." Shin replied .

OoO

Naruto was frozen in place, but not because of what he had just heard. 'I can't believe it! The Fourth Hokage is my dad?!' The old man who had come to his cell said that he was going to die, but he couldn't process that yet. He looked around from where he was, he seemed to be in some kind of sewer and there was a large barred gate in front of him with a large strip of paper with the kanji for seal on it. Naruto could sense there was something beyond the gate, but he couldn't see what it was.

Suddenly a pair of large red eyes opened from the other side of the gate. "Stupid boy, you're in danger, you need to focus." Said the Nine-tails.

"You're the Nine-tails?" asked Naruto looking up at the large glowing red eyes looking down at him.

"That should be obvious, brat." A large claw hit the gate then disappeared in the darkness behind the gate again. "Focus!"

"What am I supposed to do? I can't move!" replied Naruto, as he struggled to move any part of his body.

"Don't bother, it's useless to fight." Said Danzo appearing in between Naruto and the sealed gate. "You beast, are coming with me." he said staring calmly into the demonic eyes with his Sharingan.

" Damn those eyes. I am going to...kill you...remember that." The Nine-tails speech slowed and eyes changed to reflect those of the Sharingan.

"The attitude of a proper weapon, and I'm going to put it to good use." Danzo said as he seemed to float up towards the seal on the gate.

"NO Stop it!" Naruto cried as he tried to force his body to respond.

"It's too late, the Nine-tails is mine now." Said the old man as he began removing the seal.

Just as the seal was undone, a fist collided with Danzo's face in a flash of white and yellow.

"Damn you...Minato." said Danzo as he flew towards the wall and seemed to fade out of existence.

Naruto was able to move again but was quickly surrounded by swirling red chakra that seemed to start overtaking his body. He could feel it start invading his mind as he was starting to lose himself in the power and rage.

"Here let me take care of that." Said the tall blonde man standing in front of him. He quickly went through several hand signs and redid the seal, closing the gate and stemming the flow of chakra from the Nine-tails.

Naruto collapsed to his knees and took a deep breath. He wasn't even able to think when that chakra enveloped him. He looked up speechless at the figure before him, 'I can't believe it, it's the Fourth Hokage...my dad.'

Minato watched as his son slowly stood up, looking at him in awe. He was pretty sure that Naruto hadn't even noticed that their surroundings had changed. "Hi Naruto. I was hoping that I wouldn't have to appear here so soon. But it looks like Danzo has set his eyes on the Nine-tails. I'm sure you're wondering why I'm here." he said waiting for Naruto to say something.

"...D...dad?" Naruto asked as he could feel tears threatening to fall.

Minato smiled warmly at his son. "Yeah, that's right, you're my son. I wish I had time to talk more with you, but I need to get you out of Danzo's reach, so I need to conserve most of the chakra I saved inside the seal." Naruto was about to speak but Minato held up a hand to stop him. "Please just listen for now it's very important, I've seen everything you have so, first off you need to get out of the village, if Danzo is after the Nine-tails, he's not going to give up after having gotten this far, and next time I won't be here to redo the seal. Kakashi will help you. Second you need to find a tall, white haired ninja, by the name of Jiraiya, but hopefully he will find you first. Last there is a man who wears a mask with one eye hole, you need to be wary of him, he is going to attempt to cause great turmoil in the ninja world." Minato finished. "Do you think you can remember that?"

Naruto wasn't sure if he could, but he was definitely going to try, so he nodded. "Ok good, thanks for being patient Naruto, now if you're brief I can answer a couple questions."

'I'm not even sure what to ask.' So he asked the one thing that had bothered him all his life. "Why did you leave me all alone?" his question started the tears that had been held back.

Minato closed the distance to Naruto and wrapped his arms around him. "I never wanted to leave you, and neither did your mom. There will come a time when you meet her like this, and she will tell you what happened and why things are this way." He felt guilty about leaving this to Kushina, but he was quickly running out of chakra. "One more question, and then I need to use my remaining chakra to get you to Kakashi's place, hopefully he will be there."

Naruto looked up at his father and took his time to remember everything he could. He had seen this face hundreds of times, but in a rocky facade. "Why did you put the Nine-tails in me?"

Minato released his son and placed his hand on his head while kneeling down to look him in the eye.

"Because I believe in you. I believe that you can control this power, and that you will be an even greater ninja than me." He hugged Naruto once last time, who hugged him back. Minato stood back up and focused the remainder of his chakra to perform his famed technique, Flying Raijin.

OoO

Kakashi had gotten Ino and Naruto's clone to his apartment, which was a good deal larger than Naruto's place, and had a spare bedroom. 'I wish I have enough chakra to spare another clone to stay with them' Kakashi thought as he prepared to head out. 'It's a wonder that Naruto can create as many as he does and still have the stamina to keep going' In truth he could leave a clone, but it would be no match for an ANBU. "You two can use the spare room." He said as he showed them where it was.

Just as he was about to leave, Naruto's clone cried out. He rushed back to the spare room to see the clone writhing on the floor, red chakra seeping out of him.

"Kakashi, what's wrong with Naruto!?"

"I'm not sure but I think I need to find Naruto fast." He was about to leave, but the clone grabbed his leg.

"Don't go...he's coming here." he got out before he cried out once more then disappeared in a puff of smoke.

Ino tensed up when Naruto's clone vanished. It wasn't that she thought Kakashi would do anything to her, but Naruto had been doing wonders to calm her nerves. With the knowledge that her life was in danger she wasn't sure what she should do, so she would have to trust Naruto's sensei. 'I hope he's ok.'

'How in the world will he get here?' Kakashi thought to himself. 'Naruto's unpredictable but I doubt he could escape ANB black ops' He sighed heavily and looked at Ino. "I guess we'll have to wait. Can I get you something to drink, I'm sure this has been a long night for you."

Ino nodded. "Yes please."

Kakashi went and made Ino some warm tea. When he returned to the room, there was a crash that came from his bedroom. He set the tea down for Ino and ran to his bedroom to see Naruto sprawled out on the floor underneath the special kunai that Minato sensei had given him upon his promotion to Jounin. 'How the hell did he do that!?' He thought carefully approaching the blonde boy. "Naruto?"

"Ow ow ow that hurt. Damn it dad, couldn't you have dropped me on my feet, yaknow." said Naruto as he sat up rubbing the back of his head. By now Ino was waiting in the doorway, watching, glad he was ok.

"Your dad? What do you know about your dad, Naruto?" asked Kakashi 'Sarutobi was adamant about not letting that get around until he was old enough to protect himself from any enemies Minato made.'

Naruto beamed up at Kakashi and Ino. "I met him. My dad is the Fourth Hokage." Both Kakashi's and Ino's eyes went wide.

"How did you meet him!?" asked Kakashi stunned. 'That does explain how and why he got here though. You were truly amazing, sensei.'

"Um I'm not sure. He said he did something with my seal so that he could meet me later, but all his chakra got used up, so I won't be able to see him again, but he did say I would get to meet my mom!" Naruto's head gave a dull throb as he started to recall all of his clone's memories. "Ugh, Kakashi sensei, why do I know how to get from my place to yours? I've never been...here...have I?"

"That is a side effect of the Shadow Clone Jutsu, your clones pass their memories on to you when they dispel or get destroyed. Look stay focused, what happened to you, what did your father have to say."

"Oh yeah right." Naruto got serious, he almost forgot he was in danger as long as he stayed in the village. "Some geezer came to the cell I was in, he said he was going to take the Nine-tails out of me. I think my dad called him 'Danzo.' But my dad stopped him and fixed the seal. He said I'm going to have to leave the village, and that you'd help me. Also that I need to find this Jiraiya guy, and watch out for a guy with a mask that had one eye-hole.

"I can't believe your dad is the Fourth Hokage." said Ino, she could sort of see a resemblance in the hair be definitely not the face. 'How did someone so talented have a son like Naruto.' Though she had to admit she wasn't giving him enough credit, Naruto had made strides past the way he was from their time at the academy. She wasn't sure she could consider her progress as impressive as his was.

"I know right!" Naruto replied smiling brightly.

Kakashi had been processing the information he received from Naruto and began thinking of a plan. "Ok you two, you're both going to have to leave the village, I know it's going to be tough but you have to believe that both you're lives are in jeopardy if you remain, so no arguing." They both nodded in response.

Ino didn't want to leave be she understood the necessity, and hopefully they would return soon. "When will be able to come back, and will you tell my parents?"

"Yes I'll take care of that, but we don't have time for it now, I'm sure Danzo is making plans to find you right now, so we have to act fast." Kakashi replied. In the next fifteen minutes they had two packs ready, and Kakashi was leading them outside Konoha's wall as quickly as possible. Once they were on the outside of the wall Kakashi turned towards Naruto and Ino. He held out a pouch, "Here's some money, it should last for a couple weeks, and here's two soldier pills, take them now, and don't stop till you reach the town on the border to the west. They both did as he said. "I'm not sure how long this will take to deal with, but I swear I'll let you know when it's safe to come back. One last thing, Naruto I'd like you to make six clones and transform three into Ino, you'll have them go in all different directions. That should throw off anyone with the Byakugan traking you." Naruto did as he said, and Kakashi threw down some sort of smoke bomb that cleared quickly, but caused Naruto, Ino, and the clones to cough. There was a strange smell to the smoke. "And now all your scents match so no one will be able to track you by scent."

It hurt Naruto and Ino to have to leave, but they both steeled themselves for what they had to do. Kakashi knelt in front of them and gave them a good hard look. "You both can do this, it's what you were trained for. Look out for each other, and try to stick together. You remember what I taught you about teamwork Naruto, and don't go running off on your own." Naruto held back his scoff, but still looked a little miffed by Kakashi's statement. "Consider that an order. And Ino I'm sorry you got dragged into this mess, I'll be sure to let your parent's know that you're alright, but I can't tell them where I sent you, and you shouldn't try to contact them." Ino nodded in response. This had been the longest and hardest night of her life. If she hadn't taken the soldier pill should would love to just sleep right about now. "Naruto, for what it's worth I'm happy that you got to meet your father, he was a great ninja, and I know you'll make him proud. And a tip while you're out there, use your clones to train, gather info, and watch your back. You have an invaluable resource at your disposal."

Naruto nodded. "Ok Kakashi sensei." Kakashi bade them farewell, and returned into Konoha to meet with Sarutobi and confront the traitorous Danzo.

Naruto and Ino took of towards the western border each with tear streaming behind them for the home, friends, and family they left behind. The clones separated themselves and took off as well.

OoO

There you go, chapter 3, I really just wanted to get this day over with, a lot happened. In future chapter's I will try to make them consist of only a day no more or less hopefully. I appreciate the readers who have sent me reviews. I hope I can continue to write a story that you enjoy. Thanks to Trulyanimelover for pointing out that Fu was the Yamanaka subordinate of Danzo. (My bad, I've updated the chapters to correct this, please feel free to point of any other such mistakes.)