Imagine Nagato's suspicions being roused when one of the Emperor's subordinates walked into his office and made it clear to him as daylight that the Emperor wanted to see him - it didn't seem like a request, but a demand for his presence before the Emperor. Given the expression and forcefulness of the man who'd walked confidently into his office, Nagato assumed it wasn't a request. The Emperor was demanding his presence. He had been surprised. Really. Before that, Naruto hadn't so much as requested his presence in a long time, even when he declined to be present in some of the meetings held within this palace.
Nagato did have important matters to deal with in Amegakure. He always has. It wasn't even safe for him to be away from his country at this stage, especially with the war this man has instigated coming into the front lines. It is of importance to note that without Naruto, a war would not be gracing the Elemental Nations. Then again, he didn't loath the idea of a war. In fact, he prefers things playing in this way. He would have started it himself when time was convenient to his plans.
Without doubt the Emperor could and would thin down number of the enemies, and that would ease things for him. Without too much opposition to face, he wouldn't have to exhaust his resources and It would be easier to move about without too much resistance.
As he saw things, it was better to allow the Emperor to play his games while he readied Amegakure for the greater things to come in the new world that will be born after the war.
Nagato didn't have any problem with the Emperor - he still doesn't. He just knew that the man has no interest in his dream - peace. With his power, if he really wanted to make the dream a reality, he could have brought it closer days ago. But he did nothing. He just settled down in his royal palace, watching the world continue to rot. That was the kind of attitude that bothered the God of peace. Even so, Nagato didn't hold any contempt for the Emperor.
He does in fact respect the man for his power and achievements. An admirable trait about the man was that he didn't arrogantly boast about his achievements, nor does he go around flaunting his power for everyone to see.
Regardless, it doesn't change the situation that surrounds this country, a situation that has gripped this world of shinobi, nor does it change that he believed it isn't right for a person like Naruto to sit without care. The man only cares - to a certain degree - about his kingdom. Nothing more or less.
Gaara's crusade with Mei produced no results. Nagato didn't find that to be a surprise. Not at all. While he may no longer believe that peace can only be achieved through pain, he knew that as long as one situation remains in this world, nothing would be achieved through meaningless talks. Hence he has always declined to commit in meetings held by those two.
Having being called by the Emperor, Nagato hadn't wasted time - despite having stared at the temptation to relax just to see what the man would do if he said he was busy with protecting his country to honor his call. He decided it best to leave some things be. The Emperor has a nasty streak about him, his power wasn't just a myth senseis tell their students - it was and is the real deal.
At this stage, Nagato didn't want to tempt things. He just wanted to see through this war. He wanted to live another day to grasp peace with both his hands.
As soon as he walked into the throne room, Nagato was greeted by an eerie silence and darkness; An oppressing wave of power wrestled with him, trying to force him into submission. In fact, there was so much power floating about the hall that Nagato halted for a second to look around to see if there was something wrong.
There was none.
Having been once hailed as a god, Nagato didn't allow himself to be troubled by this greeting. There was no sense of danger, just a load of power moving about without purpose. Nagato shook it off, steeling his own chakra to breath freely as he would like.
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Uchiha Naruto: The Sage
FanfictionMadara reveals himself to be Naruto's grandfather. He infused both his cells and Hashirama's cells into Naruto. Naruto becomes strong as a result, awakening the sharingan and later the Rinnegan. I do not own this story nor Naruto.