Well, I saw this, skimmed and exited originally but I'll give some advice. You're too descriptive and not in good ways. learn to imply through words and flow better. For example:
You have to much passive tense, people AREN'T doing things, they're being observed. Secondly, you have people knowing too much where they shouldn't. We know of like Six peopel who knew and discussed Naruto's parents, but it seems like a known fact here despite the fact that Naruto was surprised to learn from the memory imprint of Minato that he was his father. Remove all traces of his mother from being mentioned, too. Naruto knew like nothing about her.
Another thing, this here:
Nami no Kuni, otherwise known as the Land of Waves,
NO. STOP THAT. It would be just the Land of Waves, because the 'Nami no Kuni'
means land of waves. Names and some techniques are one thing like Rasengan or Chidori or Kyuubi (technically) are fine but if you can use the english version of it... USE IT. Get rid of 'Neko' or the japanese honorifics. It isn't ' Orochimaru Goshuushou-sama' ITS FUCKING 'Lord Orochimaru'
Sorry, but I'm sick of honorifics and Japanese out the wazoo in stories.
Get rid of the Mizuki part. Just scrap it. He, like has been said, isn't interesting. Talking sword, even less interesting. Unless the sword is the villain possessing people or something, then keep mizuki villainous but has subtle implications that its the sword's fault or some shit.
'due to being stuck in the equivalent of a cryogenic stasis pod in the Shinobi Nations.'
NO. Do not use metaphors to things that only exist to the readers. Maybe something like 'was forced to helplessness during the destruction of her home country, locked away from the world and the effects of time thanks to the sealing technique she had been imprisoned in.'
Your OCs are also boring, I don't really care about your princess girl with her golems because she doesn't do anything. WHY IS SHE JUST GOING TO KONOHA INSTEAD OF GATHERING INFORMATION?! Again, drop the mention of Kushina being Naruto's mother. Unless you've greatly changed history, then you should emphasize that. Nobody,
NOBODY Was really supposed to know that Kushina was giving birth except a certain few as we see Kakashi is the one that jacks it up and reveals to Obito in canon unknowingly yet the golem thing knows anyhow. You also have 10 year old child teleporting into the Hokage's office and there is a lot of things wrong with that and her instantly being accepted by Sarutobi.
Also, why is Naruto chasing after these boxes with numbers on them? Its bizarre and annoying with it seeming to only be there for him to run into your OC.
Also, your 'imperium guys' Not interesting. The series already has a secret group trying to revive what amounts to a god and is super powerful. You don't need another group involved, especially one of OCs.
Really, there's too much going on and there isn't a lot to be liked. Seriously, this isn't a prologue its like 7 ideas wrapped into one instead of something to start the plot into motion. I have no idea what is supposed to be the plot and I can't really be made to care about the characters, even the canon ones.
I have no idea where you want to go with this and I frankly don't like any of the 'new' things involved because they're either Mary Sue (the amazing teleporter child) or jsut another retread of something the series already has with OCs.
Also, you don't understand how to Use Orochimaru or Kabuto. They're great characters but I don't see them in your story, just their names. Do some more research and try to bring them to life in your story if you want them used because they have a presence whenever they appear in the manga/anime but none of that is here.