Pain Throughout Remnant

Prologue

Fear.

His parents were currently fending off the two shinobi that had just broke in his home. His father, while wrestling the kunai from one of the shinobi, shouted directly to his son.

"Run now! Get out of here!"

Watching his father get punched in the face by the ninja, his mother whispered softly to her child.

"Nagato, go!"

But he couldn't; the young red-haired boy and his mother were startled by the second shinobi charging at them. Nagato watched his mother pushed him behind her as the kunai went deeply into her stomach.

"Nagato, hurry... run..." Those were her last words to Nagato before she hit the ground.

His father, while holding back the shinobi, witnessed his wife's death and bit his teeth.

"Run Nagato! Run and don't look back! Hurry!"

But, Nagato didn't do what his father ordered him to. Instead, he fell to the floor, crying while watching the shinobi stabbed his father. A second emotion was born from within Nagato's consciousness. Anger. Fear, sadness, and anger filled his head. But, he couldn't react. He just cried and weep over his parent's death. As the two shinobi neared him, Nagato saw their headband.

"Hidden Leaf Ninja..." Anger built up within Nagato after knowing that Konohagakure shinobi had just killed his parents. The shinobi's mouth moved, but he could only hear mumbled audio. Then, it happened. His eyes; the Rinnegan were activated for the first time.

Distress.

Less than three decades ago, he left the danger of his home in search of a new home. During his hopeless search, his weariness had finally caught up with him. However, if blessed by an act of God, a young girl had saved him and brought him to a cave where he met another orphan named Yahiko. The girl who had rescued him from his darkness hour was called Konan. After giving him some food, Nagato decided to stay with the two war orphans as they formed the Ame Orphans.

Together, they looked after each other and stole food to survive the elongated war. They also dreamt of a future where they were in charge of the world; they then could use their power to eliminate every single war. Eventually, the three orphans met three legendary shinobi from the Hidden Leaf Village dubbed 'The Sannin' after witnessing their battle between Konohagakure and Amegakure. Out of the three Sannin, one of them decided to stay behind with the orphans and teach time how to look out for themselves. The name of the Sannin who chose to help the orphans was Jiraiya.

During his stay, Jiraiya would teach them the three how to fish; yet he would not teach Ninjutsu to them, much to Yahiko's dismay. Then one day, an Iwagakure ninja came across their paths when the orphans went outside. The Hidden Stone Ninja demanded food and possessions from the Ame Orphans, but regardless, attacked them. Witnessing his friend's lives in danger sent Nagato into a panic state. He had not felt this way since his parent's death. Engulfed by fear, Nagato killed the Iwagakure ninja; his Rinnegan were used for the second time. Afterward, Jiraiya rushed to their aid after Konan ran back to the hideout. There and then, the Sannin saw the Rinnegan for the first time.

Because of this, Jiraiya changed his mind and for the course of three years, the Sage of Mount Myōboku began training the three in Ninjutsu. After giving them their final test, Jiraiya deemed them ready to forge out on their own. He then headed back to the Hidden Leaf, leaving the Ame Orphans to reform their nation. The three then created an organization the 'Akatsuki'. Yahiko, being the organization's leader, began urging an end to the war. Throughout the years, the Akatsuki's ranks grew in numbers and became well-known in Amegakure. It became so prominent that Amegakure's current leader, Hanzō, acknowledged the Akatsuki's rise to power and was even afraid of it.