(A/N- This is pure speculation using the canon content. If you don't like this speculation or want to add something more, you can leave your ideas in the comments.)
There had always been confusion about Kaguya and Isshiki's powers. Isshiki's fighting power was stronger than Kaguya's.
Kaguya had broken Jutsu, incredible chakra, and an unkillable body. She wasn't defeated because she was weak.
She was defeated, but they only needed to touch her. But at the same time, if Naruto had Sasuke's Rinnegan, he could've defeated her by himself.
Kaguya's main strength was her Killing All Ash Bone, but even then, Naruto was able to push her to the limits just by relying on different flavors of Rasengan.
If she wasn't pushed to the limits, would she be an idiot to erase her own space-time?
Of course not! But that didn't mean Kaguya was weaker than Naruto. Even without Killing All Ash Bone, she could defeat Naruto (without Rinnegan).
At that time, she wasn't just facing him. She was facing four people, three of whom had Six Paths Chakra.
So, naturally, she was pushed to her limits. Although the situation was similar for Isshiki, he had one advantage.
Isshiki's life was in danger, but using Karma, he was able to absorb the knowledge and experience of a thousand years, improving his strength.
Knowledge/Experience = Spiritual Energy
Spiritual Energy = Half of Chakra
Chakra = Strength
More importantly, Isshiki had both the Ten-Tails and the remains of Shibai Otsutsuki.
Isshiki, who was able to push adult Sasuke and Naruto to the brink of death, had skills and power higher than Kaguya.
On the other hand, Naruto and Sasuke didn't have the same boost that they got from the Sage of Six Paths.
Naruto's Six Paths Sage Mode sensory was like the Rinnegan, but in that battle, he had to rely on Sasuke's Rinnegan to find shrunken Isshiki.
It was obvious that losing some abilities made them weaker, but Naruto's base strength had also increased, thus increasing his overall strength using pseudo Six Paths Mode.
So, even if Isshiki wasn't as strong as he was in the later era, Isshiki should still be stronger than Kaguya.
This was just normal. So, how could Kaguya use a sneak attack to defeat Isshiki and tear him in half?
That didn't even make sense.
Now, Naruto finally found the answer. This person was able to find Earth by some unknown means, but he knew nothing about Kaguya and Isshiki.
Nor did he know that Shibai ascended to godhood on this planet.
So when Isshiki and Kaguya came here, they found a Divine Tree, and it even had a fruit.
Maybe Isshiki never expected Kaguya to betray him.
So, he just let her bring that fruit to him, or maybe, sensing the situation of the planet, he believed the fruit hadn't matured.
Regardless, he waited, but Kaguya saw this as an opportunity.
Her understanding of the Divine Tree and Chakra Fruit might not have been enough, but she ate that fruit, taking a gamble.
She won that gamble. She gained power far beyond Isshiki and killed him.
Remember, Amado understood their history from Isshiki. Isshiki was an arrogant guy.
He would definitely tell others that Kaguya had launched a sneak attack on him when he had to.
Otherwise, he wouldn't tell anyone about it.
Unfortunately, Kaguya didn't finish the job. She managed to tear Isshiki in half, but the other half disappeared.
Since the planet hadn't been abandoned yet and it could produce another Chakra Fruit, she decided to use the half of Isshiki.
She let the Divine Tree absorb that half, in the hopes that it could produce another Chakra Fruit.
Kaguya wasn't from the main family. It was Isshiki who held the seed of the Ten-Tails, which was a young Ten-Tails.
So, Kaguya needed to use that Divine Tree to produce another Chakra Fruit.
This also explained why the Divine Tree couldn't produce another Chakra Fruit quickly.
It was like using a second-hand machine to do heavy loading work. It would take a long time.
Unfortunately, by then, her body couldn't process the power of the Chakra Fruit.
Earth had the remains of Shibai Otsutsuki. Even if they were just remains, they should've had more than enough energy to overload an Otsutsuki.
Much less an Otsutsuki who had never eaten a Chakra Fruit of that level.
So either Kaguya simply gave birth to two children, or she observed humanity and learned to pass on her powers in the form of children.
Regardless, Hagoromo and Hamura were born. Kaguya, dividing her power, feared that the main clan would find her soon.
After all, she had betrayed the Otsutsuki clan's tradition, killed Isshiki, and taken the power for herself.
More importantly, she realized even if it took too long, this planet could produce another Chakra Fruit in a few hundred years.
More importantly, that Chakra Fruit could be even stronger than what she ate. So, she needed to fully digest the power of the previous fruit and wait.
Fearing the power of the Otsutsuki Clan and to speed up the process, she started feeding humans to the Divine Tree, hoping to produce another Chakra Fruit faster.
She did this so that she didn't have to kill all humans at once, but that didn't mean she was unwilling to sacrifice humanity.
Unfortunately, before anything could happen as she planned, her sons revolted and sealed her.
'So, the main family of the Otsutsuki clan has no direct method to find Earth. Either Shibai hid Earth, or it is simply too far away from them.'
'Regardless, even Momoshiki was only able to find Earth after sensing Kaguya's dimensions.'
'So for now, at least, Earth is safe.'
Naruto looked at the Otsutsuki and thought.
'Only if he dies here. He must die here before he sends any message to his clan.'
Looking at Naruto's eyes, a look of displeasure on Otsutsuki's face.
"You thief, you are too arrogant."
He raised his hand, and suddenly, several wind slashes came out of his hand, all moving towards Naruto.
Using his Sage Mode sensory ability, Naruto was able to dodge all of them.
Crack! Crack! Crack! Crack!
When those wind blades landed, they managed to cleave nearly ten meters-thick rock with ease.
Naruto instantly increased his speed, rushing in front of the Otsutsuki as he summoned two clones and used them to increase his speed.
'Sorry, Boruto! Let your dad copy your idea!'
Two of his clones struck his feet using Wind Release: Gale Palm.
The Rasengan appeared on Naruto's right hand, and a kunai coated in Wind Release chakra appeared in his left hand.
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