Disclaimer: I don't own Naruto.
Point of divergence: Kushina doesn't die in the kyuubi attack when Naruto was born. Minato was just a split second faster than in canon and Kushina didn't take a fatal blow. Obviously, Sarutobi doesn't have to deal with baby Naruto, Naruto isn't an orphan, and so forth. This is not about awesome new jutsu or how much more powerful Naruto would be. Naruto is already a BMF, he just didn't have parents around during his childhood. But what if he did? First chapter in Kushina POV. Later chapters in Naruto POV.
Chapter 1
Kushina woke up in a hospital bed. She remembered Minato finishing the sealing jutsu and the kyuubi was sucked into her son. She remembered being wounded as the kyuubi screamed at being incarcerated yet again. She had thought it had been fatal. Minato said that it looked fatal. So why was she still alive?
A nurse must have seen her eyes opened because she heard them talking about Sandaime. Sarutobi-sama would probably arrive soon with many questions that they hadn't had the time to properly answer the night of the attack. The night of Naruto's birth.
Kushina was weak, but she was alive. And she wanted nothing more than to hold him in her arms. To protect him. She knew all about what it was like to be a young jinchuuriki. She knew what it was like to grow up alone.
"Nurse," Kushina rasped. Her throat and chest hurt badly. She didn't even bother trying to form chakra. She simply searched for a call button. She was still exhausted. Her heritage gave her incredible longevity and health, but she had been injured badly. It would take some time to completely heal. As much as she wanted to storm off and find her son, she would have to rely on others.
The nurse came in and looked at Kushina. "You are an amazing woman, Uzumaki-san," the nurse said. "Nobody expected you to wake. When Sandaime-sama brought you in, you had internal injuries and suffered from severe chakra exhaustion."
"Where is my son?" Kushina asked, grabbing the nurse's arm. "Where is Sarutobi-sama?"
"Please. You must calm down, Uzumaki-san. Your injuries are severe."
Kushina's temper flared. She knew that she should rest. Objectively, she knew that it was a bad idea. But she hadn't seen her son, her husband had used a forbidden sealing jutsu that dragged him to hell to save them, and she thought that she had died. She knew better, but her temper got the better of her.
"NO! BRING. ME. MY. SON," she screamed, forming chakra and channeling it into her body. "NOW!"
The nurse screamed in pain and Kushina realized that she was squeezing the poor woman's arm with a combination of a mother's protective instincts and the enhanced strength of ninja techniques. Kushina let go of the nurse.
"I'm sorry. Please. Just bring me my son," Kushina pleaded.
"Thank the gods," came a familiar voice. Jiraiya-sensei crouched in the window. "I know that I am the boy's godfather, but I would have been terrible at it. Sarutobi-sensei would have had to do most of the work. I know nothing of babies." Jiraiya had his head hung in shame. He wouldn't meet Kushina's eyes.
"Where is he, Jiraiya-sensei? Do you know?" Kushina pleaded.
"Sarutobi-sensei is protecting him." Jiraiya stopped. "I—" Jiraiya turned away. He couldn't even look in her general direction. His favorite students had grown up, gotten married, and had a child. To top it off, they had asked him to be the boy's godfather. He knew his own faults. He knew that he couldn't be around the boy until he was older. He just couldn't. "I'm sorry. I'm so sorry," his voice was barely a whisper.
Kushina was barely paying attention. Her body was screaming in pain from her exertion with the nurse. Jiraiya was sorry. Why wouldn't he be sorry for her? Her husband, his favorite student, had died protecting the village. It hit her then. Minato was dead. Not only dead, but dragged off by the shinigami.
She wept openly. Her son was alive. Her husband was dead. She was still excited about her son, but it was bittersweet without Minato. They were shinobi. They knew the risks. But she had always dealt with it in the long term by denying the possibility of their deaths.
The nurse led Sarutobi-sama into the room. Jiraiya still wouldn't look at Kushina, but he didn't leave either. Kushina was flooded with joy at the tiny baby Sarutobi brought her. She cried harder, bringing Naruto into her uncharacteristically gentle embrace. He had blonde hair, just like Minato.
—6 months later: the apartment of Kushina Uzumaki—
"Jiraiya-sensei, it doesn't matter. I'm not dead," Kushina said.
"It matters. I heard that you two might be dead and my first thought was, 'I hope Sarutobi-sensei doesn't know I'm his godfather,' because I didn't want a baby around. You and Minato honored me and I nearly blew it off because I don't like babies," Jiraiya said fiercely. He had vowed that he would be the very best godfather possible.
Kushina paused, looking at the Sannin intent on murdering the man. He hadn't left her alone since the hospital. Naruto was finally asleep and the dolt was nearly screaming at her. He really did know nothing about babies. For being such a renowned pervert, the Sannin was amazingly uninformed about the aftermath.
"Shhh," Kushina shushed. "Naruto is finally asleep." She had a hard look in her eyes. She had recovered quickly from her injuries. A testament to her Uzumaki health. She knew that Jiraiya was wracked with guilt. At first, she had been infuriated with the Sannin, but after several months she was mostly just tired. "Jiraiya-sensei, you aren't helping. I'm exhausted. Naruto is definitely an Uzimaki. He has endless stamina and I don't have the energy to be mad at you anymore. We are safe within the village. Just go somewhere. Write your books. If you wake Naruto again, by all that is righteous and holy in this world I swear I will poison you and then beat you to death. I mean it. Come back often, but leave. Tsunade has been gone since the end of the war. You are fantastic with genin, but Naruto is only a baby."
"But—"
"I'm letting you off the hook, Jiraiya-sensei," Kushina said honestly. It wasn't the old lech's fault, really. It was like the scorpion and the frog. "Just make sure that you come back around," she added.
Jiraiya hung his head. They had had this conversation many times before, but he could tell that the Red-Hot Habenero was no longer angry with him. He would have deserved it if she had held a grudge forever. He knew that. After the first time Kushina had forgiven him, he'd made the vow. He intended to keep it, but he couldn't fight her anymore. She was right. He hated that she was right, but he admitted it. "You're right. I'm not helping. I will not fail again. I will return."
Kushina sighed. "I almost wish you'd just go peep at the hotsprings so I could have some peace," Kushina muttered. She was too tired to be offended by the old lech. She fell asleep where she sat on the couch leaving Jiraiya to wonder if she'd meant it. Jiraiya made sure to secure the apartment before he left.
—Playground in the Leaf Village; Naruto, age 4—
"Hi! My name's Naruto Uzumaki!" the boisterous blonde boy shouted at the other children in the sandbox.
Kushina was sitting on a bench watching her son. His spikey blonde hair reminded her so much of Minato. It had been four years and she still missed him, but his absence hurt a little less. Sandaime had been very generous with their stipend and she hadn't been on a mission since before she was pregnant. She still trained, but she hadn't been in the field in years. Every time she got restless, she would look at Naruto and the restlessness melted. She knew that he needed her.
The other villagers always whispered and avoided him. It was supposed to be an S-ranked secret, but somehow it had leaked to the general populous that Naruto was the kyuubi jinchuuriki. She understood their hatred. It was callous and uninformed, but she understood.
At first, she had challenged the villagers who stared and whispered. But it didn't really help any. Naruto would just have to grow up and prove to them that he wasn't the kyuubi. Her ninja friends, on the other hand, were much easier to persuade. She explained to them that Naruto was just a boy, that being the jinchuuriki didn't mean that he was the kyuubi.
She found out who her true friends were, not that she was surprised at who remained. Mikoto Uchiha was one of them, although her husband wasn't. Shikaku Nara had said, "Troublesome," in an understanding tone. She was never close friends with the Hyuuga, but the Hyuuga were more outraged that she refused to remarry and raised Naruto alone than whether Naruto was kyuubi. Of course, Minato's sole surviving student, "Copy" Kakashi Hatake, didn't care. Kushina asked him to visit, but she found him more often at the memorial stone for the Third Great Ninja War.
She shook herself from her reverie to see that Itachi and Sasuke were playing with Naruto. Sasuke and Naruto were both trying to catch Itachi. They were having so much fun that she barely noticed the ANBU in the tree at the park. She saw Mikoto watching the children play with Itachi. Itachi was already a Chunin and Mikoto had bragged that he was applying to ANBU.
Kushina body-flickered to a branch next to the ANBU. "Are you here for me or Naruto?" she asked. The ANBU just shook his head. Kushina body-flickered back to her position on the bench and continued watching Naruto play.