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Pakkun is the personal summon of Hatake Kakashi. Kakashi called on Pakkun and the nin-dog pack to track and capture the Missing-nin Momochi Zabuza. They managed to bite onto the missing-nin and pin him in place. This allowed Kakashi to use Raikiri without fear of a counter attack. Some months later, Kakashi called on Pakkun to track down Uchiha Sasuke for Naruto and Sakura. He would watch from the sidelines in surprise as Naruto and Gaara rampaged through the forest.

A short time later Pakkun and his fellow nin-dogs would be called upon by Kakashi to track down Naruto and his team who had gone off in pursuit of Sasuke. Pakkun caught their trail and he and Kakashi went in pursuit. They did not arrive in time though, as Naruto was defeated and Sasuke was gone. Pakkun and Kakashi talked of the meaning of the Valley of the End and how the lives of the men honored there mirrored those of Naruto and Sasuke.

Several years later Pakkun and the nin-dog pack were called upon to track down Akatsuki member Sasori using a small piece of his clothing.

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Pain was a Hidden Rain missing-nin who was rumored to come from the Fuuma clan, note this is a different clan than the one located in the Rice Field Country. Pain was once a young Rain orphan named Nagato. During his youth in the war torn Rain Country, he met fellow orphans Konan and Yahiko. Nagato was a quiet child who admired Yahiko's desire to improve their living conditions and bring some justice to the world. Nagato and his companions met the Sannin following the war with the Rain Village. Jiraiya took a liking to the children and stayed behind to look after them. Jiraiya was surprised to learn that the emotional and quiet Nagato was a wielder of the Rinnegan, the venerated Doujutsu once possessed by Rikudou Sennin, the man regarded as the original modern shinobi.

Nagato and Yahiko were accosted by a vagrant Rock Ninja, and Yahiko moved to defend them. He was defeated and Nagato went into a berserk rage, quickly killing the ninja. Nagato was shocked when he finally regained control and Jiraiya promised to train the orphans so they could defend themselves. Nagato had trouble dealing with the way he reacted to the Rock ninja and Jiraiya explained that he shouldn't feel ashamed, as he was defending his friend. And that knowing what it feels like to be hurt is the reason why humans are kind to others. Nagato wondered how he could become like that and Jiraiya explained it just came with age. Nagato then promised to keep his friends safe, no matter what pain he had to experience. Three years passed and the trio were soon skilled enough to defeat one of Jiraiya's Kage Bunshin. He explained his time with them had ended and that hard times would still be ahead for them. But by working together they could change things, as they had finally grown up.

Over the following years the trio entered many battles and rumors emerged that they may have died. Nagato continued to develop his skills and his Doujutsu and took on the name of "Pain". As Pain, Nagato began to gather other disenfranchised Rain shinobi and start a civil war with Hidden Rain. This apparently was a plan in line with Yahiko's expressed goals. Though Rain was led by legendary ninja Sanshouuo no Hanzou, Pain managed to kill Hanzou. He did not stop with merely Hanzou though, for he killed Hanzou's family, friends and associates; essentially taking down Hidden Rain all by himself. And though Pain had followers, they never saw Pain personally. His abilities, appearance and heartless nature thus fueled rumors about his identity. This also caused his followers to revere him as a god. In this position he operated out of the tallest tower in the Rain Country industrial city. In this tower he also maintained a secret room containing six mysterious beds, five of which held figures in Akatsuki cloaks.

Some years before Pain also became a part of the Akatsuki organization. Konan joined as well, and was one of the few living persons aware of Pain's past. In this position she had seen him fight many battles and believed that he had never once lost in battle. She and his followers were also aware of his ability to control the rain which fell around their location. This he apparently did on schedule, so when rain fell on other days, his followers knew something was on his mind. This rain also had the ability to detect the chakra of opponents and allow Pain himself to feel their presence.

During the Akatsuki meetings, Pain was adamant that the group could fulfill their desires if they possessed the bijuu. In his position as leader, he was shown to use a Shouten technique, which allowed the group members to take over the sacrificed body of another in exchange for some measure of their chakra. He also was responsible for summoning the huge King of Hell statue which holds the spirits of bijuu withdrawn from Jinchuuriki.

Pain has stated the group's ultimate goal is to control the world, but this may actually be a smokescreen, as Pain has been seen to report to Tobi in secret. Tobi directed Pain to capture Naruto personally in his role as leader, which apparently drew out an emotional response from Pain in the form of rain. Pain has officially told the group their goals can be accomplished through three steps. Step One is for the group to attain money. Step Two is to create the first mercenary group. Shinobi villages make money for their country, and for the money to be steady it requires war. Because there have not been any large scale wars in approximately the last decade, the ninja villages were being reduced in size. The Five Great Shinobi Villages could handle the downtrend, but the smaller villages could not. Akatsuki will form their own fighting force with no country allegiance. With this force they will undercut all the other villages and fight their battles for cheap. Then using the bijuu they can create new battles and new wars and gain a monopoly over the whole market. In the end they plan to control all the wars and be powerful enough to even collapse the shinobi villages of the large countries, forcing them to rely on Akatsuki as well. With all that in hand, the group can achieve Step Three, to control the world. Whether this aspect of the plan is true or not is unclear.