Yo! Before we start with the story, there are some things to clear:

1) Naruto is four years older. he is sixteen when Konoha 12 graduates
2) He is a natural genius much like his father or Kakashi
3) He knows about his parents, Kakashi is like an older brother to him, Jiraiya and Tsunade are his Godparents
4) Naruto doesn't have the Kyuubi, but his Chakra reserves are still huge due to his Uzumaki blood
5) Konohamaru is older than in canon, he is the same age as Konoha 12

Besides this, there are still no pairings, so if you have any suggestions, please write it in reviews!

I am gonna say this only once: I don't own Naruto!

"Talking"

'Thinking'

"Jutsu"

'Flashbacks/ memories'

"Summon/Biju talking"

'Summon/ Biju thinking'

Naruto of the Flash Step

Chapter 1: Beginning

Shouts and yells were heard in the waiting area in which a young, blond boy and a white-haired man were sitting. The boy's hair was long and spiky, just like his fathers. His sharp, azure blue eyes looked at the door in front of them in worry. The boy was wearing a dark blue, short-sleeved shirt with a red spiral in the middle and black pants. He also wore black sandals. The boy was four years old and his name was Namikaze Uzumaki Naruto, son of Namikaze Minato, the fourth Hokage and Uzumaki Kushina. The man, who was sitting next to Naruto was his Godfather, Jiraiya, one of the three legendary Sanin and the Toad Sage.

The two of them were in a hidden cave which was known only for a handful of persons. You could ask why they were here, well, Kushina was pregnant again, this time they would receive a daughter. As the two waited until either Minato or Tsunade would come out to get them, they heard a scream followed by Minato's curse. While Naruto didn't know what was happening, Jiraiya quickly stood up and rushed into the room.

When he entered, he saw a cloaked man holding Naruto's sister with a Kunai held to her throat. On the other side of the room, Minato and Tsunade were standing in front of Kushina who was looking very tired.

"Minato! What is going on here?" Shouted Jiraiya, wanting to know who was attacking them., but Minato ignored his Sensei and tried to calm their attacker.

"Please, calm down, there is no need to do that!" Minato told the cloaked figure, but all he got was a shout of 'I am as calm as I can get' from the cloaked person. In the next moment, the cloaked men threw Naruto's sister into the air and prepared to stab her, but before he could do it, Minato appeared next to her and jumped back. Suddenly he heard a hissing sound and looked at the blanket that was covering his daughter.

With fast thinking, he used his most priced technique and teleported into one of his safehouses, leaving the two Sanin with Kuhsina and the cloaked person. Jiraiya turned to Tsunade and nodded to her and she rushed at the man who simply phased through her punch like a ghost. Suddenly Jiraiya was in front of the man with a Rasengan in his right hand and tried to hit the cloaked man but it happened the same thing as with Tsunade.

"Hmph, I thought that the two of you would be a bit better," The cloaked person said and rushed at Kushina, with his right hand extended, but right as he about to touch her, he phased through her again as Tsunade tried to punch him in back of his head. The cloaked person jumped back and made a set of hand seals pointing at Tsunade and Kushina.

"Katon: Great Fireball Jutsu" The Cloaked person exhaled a large orb of fire which flew directly at Kushina and Tsunade. Jiraiya was about to start his own hand seals but then everyone heard another voice.

"Suiton: Water Wall Jutsu!" Naruto shouted and spat out a large amount of water in front of his mother and godmother, protecting them from the fire Jutsu. Naruto suddenly took out a Kunai and threw it at the cloaked figure. As expected, the knife passed through him, but no one expected Naruto to suddenly substitute with the throwing knife and punch the man in the head.

To everyone's shock, Naruto's punch didn't phase through the cloaked person. The cloaked man stood there for a second in shock before he released a grown and turned around and hit Naruto with an uppercut to the young boy's abdomen, which made Naruto spit out blood and salvia. As Naruto slid of the mand arm and hit the floor, the last thing before everything went black was the cloaked man grabbed his mother and they both vanished in a swirl.

1 year later

One year has passed since one of the most tragic days of Konoha. Exactly one year ago, the Great Kyuubi no Yoko, the greatest and strongest of the Tailed Beasts attacked Konohagakure no Sato. Many people died in the fight with the beast, but there were only three people who Naruto cared about.

The first one was his mother who died after having the Kyuubi extracted from her, but not before helping in sealing the beast again. The other one was his father who died protecting the Village by summoning the Shinigami and sealing the Tailed Beast. The last one was Naruto's little sister who died because of a heart attack caused by the Kyuubi's Killing Intent focused on her.

one year after Naruto's family died, he was heartbroken, everything he loved died in one night. His parents while sealing the beast. His sister for who he waited a whole year because of the beast. His Godfather had almost no time to stay in Konoha as he had to maintain his Spy network since the leaf was weakened now. His Godmother had become the Hospital Head and had almost no time to be with him in these hard times. His Grandfather figure, Sarutobi Hiruzen, become the Hokage again and he had to take care of his family and the Village as well.

But that didn't keep Naruto down for too long. he realized that crying will not help with anything. Since then he started to train, every and single moment he had for himself he spent training. Either training physically, learning new taijutsu Katas, learning new Ninjutsu, learning Fuinjutsu from his father and mother notes or even simply reading about everything about being Ninja.

He did it all because every time he remains himself about the dreadful night, he always comes to the same conclusion about the fight.

He was useless.

He couldn't protect the people he loved.

He was weak.

That was the reason why he trained so hard those days. It also helped to have an older brother figure who was a Jonin and often could give him some tip and advise.

And now here he was, sitting in a classroom, full of kids who were hoping to become Ninjas of the leaf. Naruto wouldn't say that he was antisocial, but sadly he couldn't remember any of their names. Well, while he didn't know anyone, everyone knew him since he was the son of the Yondaime. Of course, like every popular boy, he had his fan club, which he rather would like to avoid for some more time.

As their Sensei enter and started the lecture about the history of the leaf, Naruto dozed off. He knew it already and the teacher knew it, because every exam they had him write, he always scored a 100%. That was the reason why Naruto didn't bother to listen to the teacher. Besides he had better things to do.

As Naruto closed his eyes, he started to replay the night of Kyuubi attack. Naruto often did that, so that he can analyze the fight again and again. he didn't know why, but the ability of the cloaked person was intriguing Naruto to no end. The ability to phase through people, Jutsu, and walls. It was a crazily powerful ability. If he could be able to replicate it, he would be always able to protect the people he loved.

But first, he needed more knowledge on Fuinjutsu to be able to do something like that.

For now, he had to focus on the basics.