I'm sorry to say this isn't a an update. Well, it kinda is.
On one part, I'll say it immediately : this story is up for adoption. Why, you may ask ? Several reasons.
First off, college. I don't have as much free time as I used to be.
Second, this fanfic is a testament to my former fondness of bashfics. I won't lie, I'm not no longer fan of these, and thus, continue a « Naruto is betrayed by Konoha » stereotypical fanfic would be superficial.
Third, my old writing is objectively atrocious. If anyone ends up adopting it, I'd suggest to see where you can improve on it.
Finally, it has good ideas, and I truly regret abandoning it, but I really, really don't think I could give the story justice if I continued it.
Thus, I'm going to give you ideas of what I originally planned, so that I don't leave you guys hanging (if you adopt the story, you don't have to follow these suggestions. It's up to you whether or not you want to follow these) :
The teenager Haku found unconscious ? Yeah, it's Ninten from Earthbound Beginnings / Mother 1. He came there as he was investigating strange activities seemingly linked to Giegue/Giygas. Upon leaving Konoha, Jiraya and Naruto meet Haku and Ninten, before the four of them meet Kimimaro shortly after. They end up going back to Ninten's home in a parallel dimension, in Podunk. They train for years up until the Chunin Exams, hoping to use Haku and Kimimaro's PSI abilities as a factor against Giegue.
A key plot point would be the lack of unity against Giegue. Due to the fact that Hidden Villages and Akatsuki being in conflict with each other, Giegue can silently continue his invasion of Earth undetected. Naruto and Jiraya are part of this reason, as their refusal to work with Konoha due to their grudge against it is seriously damaging.
Sasuke, Sakura and Hinata end up in conflict with Naruto, due to the latter's loathing of Konoha. None of them is thrilled about it.
Surviving the Uchiha massacre due to being away when it happened, Kasumi is left a bitter, misanthropic child who's only attachment is to Sasuke, Sakura, Hinata and Naruto. She can use PSI like Ninten, but and it's precisely because she knows PSI (as well as the fact that Kimimaro and Haku knows PSI as well) that Giegue is in the Elementary Nations and planning a full-scale invasion (ordered by his people to destroy them to prevent PSI from falling in human hands). Where she learned it or from whom she inherited it is a mystery. Imma leave you guys ideas on how she got it.
Not being a Mary-Sue and suffering from the Curse of Hatred, without a healthy way to deal with her anger, Kasumi ends up joining Giegue. She won't be redeemed, but she still loves her friends Naruto, Sasuke, Sakura and Hinata, and constantly tries to capture them so that they could join her. Neither Kasumi herself nor her friends are willing to harm each other, screwing their respective sides in the long run.
Lloyd/Loid, Ana and Teddy are introduced during the Chunin Exams. They came back to the Elementary Nations with Naruto, Jiraiya, Ninten, Haku and Kimimaro. They are constantly wandering around the Elemental Nations to discover Giegue's plans and stop him.
Hiruzen, due to his experience, is a genuinely cunning villain, and outsmarts Jiraiya and Naruto several times. However, his power-hungry attitude leads to him to try and take control of the shaky alliance against Giegue, leading to conflicts and divisions within the Alliance.
The Earthbound Beginnings / Mother 1 characters' mentalities enters in conflict with the shinobi alliance against Giegue due to their vastly different morals, leading to a shaky alliance.
Giegue will be immune to singing unlike Earthbound Beginnings / Mother 1.
Giegue, for some reason or another, completely loses his mind, leading to to the events of Earthbound/Mother 2.
I must apologize for choosing not to continue this story, but I believe that my current mindset won't allow me to give this story justice.
Have a great day !