Disclaimer: I don't own Naruto.
"He can't be swayed and I have tried my best, Minato," Mikoto said sadly. This is the only option, I'm afraid.
"Mikoto…" Minato pleaded. I don't want to force you to choose between us.
"I know my duty, Hokage-sama," she stated with an air of finality. It's not you who is trying to make me choose one of you.
Minato watched his former teammate lean back in her chair. She evidently thought that the discussion was closed.
"Do you have any idea what will happen to you?" he asked. This isn't fair on you.
"It does not matter. This will be my sacrifice for the village," she replied. Life isn't fair unfortunately.
She got up and turned to leave.
"What about your sons?" he questioned. Change your mind for them at least.
"You may tell Itachi and he will explain it to Sasuke when he is older. Take care of them, please," she told him. You know they're the other reason I'm doing this.
He stared blankly as Mikoto disappeared in a swirl of leaves. Sometimes he wished he wasn't Hokage.
Four days ago, the Uchiha elders and clan head were killed during a routine meeting. Yesterday, Uchiha Mikoto was officially listed as a S-class missing-nin.
The Hokage had requested a meeting with Uchiha Itachi. This intrigued Itachi enough that he turned up even earlier than usual. He hadn't met the Hokage as just Itachi since he'd joined ANBU several years ago.
"In two days' time, I will be forced to list Uchiha Mikoto as a S-class missing-nin due to her recent actions," the Hokage said, looking at Itachi for a reaction.
He nodded, confused. Was this all the Hokage had wanted to say? Of course this would happen.
Apparently not, as he continued speaking, "As you might know, I was working with her in an attempt to prevent an coup by the Uchiha clan."
Itachi does know because his father believes that there are certain things the heir must be aware of and a conspiracy to overthrow the Hokage is one of them. He had not realised the sudden tension between his parents was due to it though. In retrospect, he should have because his mother may have loved his father but the Hokage had been her teammate first. She would not stand by and see him replaced (killed) easily.
"However, she had despaired of finding a solution until Danzo made an unwelcome suggestion which then she adapted to her needs," the Hokage finished.
"What was the suggestion?" Itachi asked.
"Danzo proposed that ANBU should wipe the entire clan out and with your skills, you would be the most logical choice to carry out such a task. Mikoto was not in favour of this for obvious reasons and decided that she would deal with the ringleaders on her own, with or without my approval," the Hokage replied.
"She did her duty to the village, Hokage-sama," Itachi said. "If that is all, I have clan business to attend to."
"Dismissed," the Hokage told him.
When Itachi is gone, the Hokage becomes Minato again and ponders what Mikoto gave up for the village.
Mikoto did not have long to wait outside of the bath house in a remote town. She'd followed Jiraiya's trail for several days now. She suspected he knew that someone was tracking him but doubted that he realised it was her.
He looked older and more tired than she remembered but then she hadn't seen him since shortly after Sasuke's first birthday. Stepping out of the shadows, she said, "I knew I could find you here, ero-sensei. Could you give Minato a message, please?"
"Mikoto? Why?" he asked. Why did you kill your husband? Why did you make your sons orphans?
"Sometimes your loyalties conflict and you must think of the greater good," she replied. I didn't want to leave them alone. It was the only way.
He studied her, frowning but told her, "I'll take your message." Was it really? What actually happened?
"These are for Sasuke, his birthday is soon, and this is for Itachi with my congratulations," she continued. I can't talk about that.
He was handed several packages.
"I'll see you around, ero-sensei," she said before she disappeared.
Jiraiya watched her go, thoughtful. It looked like he needed to have a talk with Minato.
"And my dream is to find a certain woman," Sasuke finished.
Kakashi blinked, Naruto looked bored and Sakura regarded Sasuke with awe.
Great, so I have a fangirl, the Hokage's son, and an Uchiha with mother issues. I wonder why Kurenai and Asuma got the normal teams. Sensei is obviously punishing me for something or else he has a lot of faith in my teaching abilities.
"Well, that was interesting and all, but tomorrow is survival training. Meet me on Training Ground 10 at nine and don't eat lunch."
Hana watched the trees warily. She was sure that someone was there even if she couldn't see them. This tracking mission had proved to be trickier than she first thought and she didn't want more complications.
"Are you looking for me, Hana? You wear the fan very well indeed," said Mikoto as she dropped out of the branches.
Uchiha Mikoto was one of the most dangerous missing-nin outside Akatsuki. Her infamy in Konoha was only eclipsed by Orochimaru's. She tended to keep a low profile though so for her to come so close to Konoha was interesting to say the least.
"Tradition. You're not being hunted hard," Hana replied.
Why is she here? And where are the ANBU that are supposed to stop this kind of thing happening?
"I have my ways. This is for the child," Mikoto stated, dodging the implied question.
Ways? Wasn't she the Hokage's former teammate? She would have to ask Itachi later. And how did she know about her child? Actually, Hana thought, that was probably easy to figure out. The birth of a heir to a prominent clan was always big news and ninja were shameless gossips.
"Have your ways, my butt," Hana muttered as Mikoto substituted herself for a stuffed weasel.
Now that was taking a joke too far. A stuffed weasel? Well, she supposed that few other children got presents from missing-nin grandmothers so there was that at least.
And cue the ANBU. She wondered where they'd been earlier.
She went through the usual questioning. She explained that yes, they had just talked. No, she hadn't tried to apprehend Mikoto. Did she look suicidal to them? What was that? It was a stuffed weasel that Mikoto had given her for her first child. She firmly told them that it wasn't a) stuffed with explosive notes b) contained a listening device or c) designed to cripple the inner workings of Konoha in some other way. It would go home with her and not back to ANBU headquarters to be taken apart.
After all that, she finally remembered why she was actually there in the first place. Her target was probably long gone. Wait, was that one of her dogs? Yes, he did have Tora in his mouth after all. Mission accomplished.
This wasn't the first time Sasuke had gotten involved in the same battle as his mother. For someone who supposedly kept a low profile, he had seen her around in nearly every major battle he'd been in. However this was the first one where she'd actually picked his side to fight on.
She was very good, he thought, watching her taijutsu. Oh, he'd known that she'd been trained by one of the Sannin and killing his father would not have been easy but he still regarded her as the woman who raised him and hadn't been an active ninja since before Itachi's birth. This was probably why he heard the screamed warning too late and looked up to see Samehada about to take his head off. Suddenly there was a pop of a shunshin jutsu and somebody in front of him who collapsed on top of him. He rolled out from under them and discovered it was his mother with a large hole in her chest who had taken the hit for him. She smiled at him and closed her eyes.
Itachi looked at Sasuke. Sometimes he wondered what teaching methods Kakashi had used because his brother seemed completely incapable of looking 'underneath the underneath' as soon as his emotions got involved.
"Do you understand now, little brother? She sacrificed herself for our future," he finished.
"Yes," Sasuke stated.
Do you really? Maybe one day, you'll be able to think of it objectively but I doubt it, Itachi thought.
Two days ago, her sons carved Uchiha Mikoto's name on the memorial stone after a long and bitter fight with their clan.
hides from angry reviewers
I think this is a Sandaime seals Kyuubi!AU but it doesn't matter why Minato is still alive. It is important that he is though because I can't see her doing this if he wasn't Hokage. Also he would be less likely to order Itachi to do the massacre.
The idea of them being teammates is my personal theory.
Couldn't resist sneaking a bit of ItachiHana in. Can you substitute yourself for something that isn't a log?
I don't know how she managed to kill them but she's very tricky in my opinion.
Edited 22/10 because FFFX pointed out that it needed a lot more detail. Also he mentioned something important. Mikoto isn't a blood Uchiha here because that would make her end up being recruited by the Akatsuki and that is drastically different to my vision of the plot of this story. She might be one in canon, I don't know.