Naruto Shippuden Story and Ending Explained

Naruto Shippuden is the second series of Naruto anime that follows the titular hero on his quest to become Hokage. Unlike the first series, Naruto is now older and has new teachers to help him through his adventure. At the same time, he faces the biggest threats to the five shinobi nations and must deal with the loss of someone he considers a brother.

While the original series was filled with serious issues, Shippuden dialed everything up a notch, thrusting Naruto into a world of war, death, and betrayal. He’s not a kid anymore and the gloves have come off.

Shippuden is finally coming to an end though, and with all of the story threads getting tied up, it can be a lot to take in. The anime and manga throw a lot at fans in order to explain the events at hand. For new fans, and those who may not remember everything from hundreds of episodes ago, we put together a simple explanation of everything that you need to know in order to understand what’s happening.

Naturally, there’s a lot of information that can come out of such a long series. With that being said, we’ll focus on the most pertinent bits to provide you a better understanding of the overall picture.

Needless to say. There are some serious story spoilers for Naruto Shippuden ahead. 

Naruto and Sasuke

One of the primary focuses of Shippuden is the relationship between Naruto and Sasuke. Both were outcasts who formed an unlikely bond thanks to their dreams of the future. The need for power was clear, and each set out along with Team 7 member Sakura and teacher Kekashi to reach their goals. Unfortunately, as the original series came to an end, it became clear that each sought power for very different reasons.

Where Naruto wanted to earn the love and respect of the village as well as protect his home, Sasuke wanted nothing but vengeance and control. As Shippuden progresses, the two begin to but heads more and more until Saskue finally takes his leave to join the likes of Ochimaru. This distance between the two friends plays a heavy role throughout the series as well as the end. Both are avoiding what must be done, and that building conflict will define the men they are going forward in life.

Both of the young men actually have a deeper bond that becomes clear nearer to the end of the Shippuden series. They embody the spirits of Indra and Asura, sons of the founder of shinobi. Those two are pit against one another in an eternal war, waiting for the cycle to be broken by two who are strong enough to put their differences aside. 

The Akatsuki

The Akatsuki are a band of rogue ninja organized for a specific mission. They have been ordered to collect all nine of the tailed beasts, although throughout most of the anime nobody knows why. It’s clear that each beast possesses enormous power, but the members of the Akatsuki aren’t after the spirits for themselves. Instead, they are collecting them to place in a vessel known as the Gedo Statue.

Of course, those that house the tailed beasts, known as the Jinchuriki, are no easy targets. These are well-trained ninja with tons of chakra who have been tasked by their nations to house what are essentially weapons of mass destruction. To stop them, the Akatsuki is made up of the strongest shinobi out there, some of which are quite legendary. There numbers include Sasori, a puppet master of the sands, and Itachi Uchiha, Sasuke’s own brother (to whom he vowed vengeance).

Their leader is unknown throughout most of the anime, although it is believed to be the masked man named Tobi. This individual has mysterious powers that allow him to teleport and completely avoid all attacks. He acts as a fool outwardly, but he is clearly very powerful. In fact, it was he who caused the destruction to Konoha Village that led to Naruto becoming a Jinchuriki and the Fourth Hokage’s death. 

Naruto’s Training

With the Akatsuki becoming more active during Naruto Shippuden, Naruto himself needs more training, especially when it comes to controlling his immense power. Over the course of the series, he has several teachers. His primary ones were Jiraiya (who he lovingly called the Pervy Sage) and Kakashi Hatake. Each one was charged with helping Naruto hone his abilities after his schooling was complete.

Through missions given by the Hokage and other special journeys, he was kept away from the prying eyes of the Akatsuki so that he can prepare to do battle with them. Yamato, a ninja imbued with the cells of the First Hokage, is also called in to help with Naruto’s training in order to keep the Nine Tails inside of him at bay.

After much time has passed, Jiraiya takes Naruto to Mount Myoboku to learn the arts of the Toad Sage. This is done to give Naruto a better control of chakra, and to help provide discipline for the young, brash ninja. 

Sasuke’s Training

While Naruto was undergoing his own special training in order to accomplish his goals, Sasuke was trying to increase his power. Unlike the series protagonist, however, Sasuke was willing to use dark means to do so. This meant turning to Orochimaru.

Orochimaru is a member of the legendary Sannin (as is Jiraiya), and a former member of the Akatsuki. He wants nothing more than to find the secret to everlasting life, and is often intrigued by powerful shinobi. This leads him to want to learn from them and add them to his collection.

He helps Sasuke tap into his inner power while also trying to warp his mind so he can use him and eventually murder him. Sasuke gets the drop on Lord Orochimaru though, killing him. His training then takes him to more unsavory teachers. Joining the Akatsuki puts him in contact with Madara who promises to show him the Uchiha’s place in the world.

Sasuke is a lot smarter than he lets on, though, using each opportunity as a stepping stone for him to find his own understanding of the world and the events that helped mold him. 

The Five Kages

The five Kages are the leaders of the main shinobi villages. This is something that is learned well before Naruto Shippuden begins. However, they play a much larger role in Shippuden than they did before. While it was known that they are leaders of their respective nations, they must now work together thanks to transpiring events.

The Tailed Beasts that the Akatsuki have been stealing belong to the villages. They are checks against other nations, so losing one puts your entire home at risk. When they start getting taken, everyone becomes tense. It’s an act of war to take someone’s strongest weapon, so there is unease. That unease is exactly what the Akatsuki wanted. During the Five Kage Summit which took place in a samurai village (for neutrality’s sake), they were attacked.

Thanks to the wisdom of some wise friends, the Kages do eventually realize what’s going on. They form the Allied Shinobi Forces, which combines the forces of the lands of Lightning, Water, Earth, Wind, Fire, and Iron (a samurai nation). It was something that the Akatsuki couldn’t predict and would be the start of the Fourth Great Ninja War.

The Fourth Great Ninja War

The Fourth Great Ninja War is the first one that wasn’t fought between the shinobi nations. In the past, feuds were birthed and that pit ninja against one another. They would fight for control of Jinchuriki and Kekkei Genkai (family specific abilities). For the first time, they were united instead, facing a threat much bigger than they could pose to each other.

On one side stood the five shinobi nations along with the Land of Iron. On the other stood the Akatsuki along with their mysterious leader, Tobi. Tobi, who seemed silly at first, proved to be a much larger threat than anticipated. His power was unparalleled, and he had managed to capture at least part of eight of the Tailed Beasts. That meant the Gedo Statue was almost ready to achieve whatever its true purpose was.

Fighting alongside the allied forces were the Five Kages, although they would have a very specific target in the form of the Akatsuki’s leader. That would change, but we’ll get to that shortly. 

Sasuke’s Path

While Naruto and the rest of the Shinobi are busy building an army, Sasuke is doing his own thing on the side. After ridding himself of Orochimaru, he grabs a few of his experiments to form the group Hebi. Suigetsu, Karin, and Jugo join Sasuke to help him find Itachi so that he can finally exact his revenge.

After finding Itachi and discovering the truth of his actions, the group gains a new focus and a new name, Taka. They are now determined to take down the Hidden Leaf for its involvement in the wiping out of the Uchiha clan. To achieve his goals, Sasuke joins the Akatsuki and even attacks his former village on several occasions.

His time with the Akatsuki also reveals the true mastermind behind the organization, Madara Uchiha. One of the old leaders of his clan, thought to be dead for decades, is the one pulling the strings from the shadows. He is connected to the Gedo Statue, using its chakra to sustain his life. He shows Sasuke even more of the Uchiha’s history in order to gain a powerful ally. It would turn out that his pushing Sasuke would force the young shinobi to seek yet another path on his quest for the truth and vengeance. 

Madara Uchiha and Hashirama Senju

Late into Shippuden, the story of two young ninjas is shared, and with that, all begins to come clear.

Before there existed any of the five nations, there was always war. The two most powerful clans were the Uchiha and Senju. Each one was at each other’s throat, fighting battle after battle until one day two young boys meet. Those boys were Madara Uchiha and Hashirama Senju.

Their bond transcended enmity and that allowed for the first great ninja village, Konohagakure (the Hidden Leaf). Hashirama was perfect for leadership, having shown loyalty and kindness to everyone, and he was chosen to lead as the Hokage. Madara, being his friend, also agreed that he should lead. Over time, though, a rift grew. Madara wanted more power and felt that he and his clan were being snubbed.

Madara faced off against Hashirama and was defeated. Believed to be dead, time continued on with him plotting his revenge from the shadows. Thanks to an ancient Uchiha tablet, he knew what he had to do. This tablet shared the fate of the Uchiha and their purpose in the world. Although, it’s true meaning wasn’t shared until much later.

Impure World Reincarnation

The Impure World Reincarnation summoning jutsu, a kinjutsu (forbidden technique), is what balanced out the Allied Shinobe Force and the Akatsuki. It is much different from a normal summoning jutsu since it is able to bring back anyone with all of their abilities in tact but none of the weaknesses. What made it forbidden, however, is that you needed a living body as a sacrifice and users would most likely try and control the souls they’ve raised.

This is how the Akatsuki managed to bolster its numbers. All of the shinobi had teamed up to form the Allied Shinobi forces, leaving nobody left to fight on the enemy side of the war. So, being the geniuses that they are, the Akatsuki use all of the enemy’s dead warriors as their army. They even revive the Seven Ninja Swordsmen of the Mist, the most powerful swordsmen ever in the history of Shinobi.

It’s unfortunate that this jutsu helped the bad guys amass such power, as it was actually created by the Hidden Leaf’s Second Hokage. Once Orochimaru, and subsequently Kabuto, got a hold of it, the technique was perfected and made even more powerful. 

The First Four Hokages

The Impure World Reincarnation wasn’t all bad, though. I mean, yeah, sacrificing others just to bring someone else back is pretty low, but some good did come out of it. Sasuke, who now was looking for direction in life, needed to know the truth behind Itachi, the Hidden Leaf, the Hokages, and the Uchihas. For this, he turned to Orochimaru (who had been brought back by Kabuto through Sasuke’s curse mark).

Orochimaru summons the four Hokages and forces them to answer any questions that Sasuke may have. He is now even more intrigued by what Sasuke may have in store for the future and vows to help him.

After a long conversation with the Hokages, Sasuke finds them to be honest and lets them join the battle against the Akatsuki, while he himself finally makes a decision. He will become the next Hokage. 

Tobi’s Identity

Once the war is fully underway, Tobi’s identity is finally revealed; he is Obito Uchiha. Obito was once a team member of Kakashi’s group and was believed to have died during a mission when they were both young. In fact, he is the ninja who gave Kakashi his Sharingan (something only possessed by the Uchiha).

After the accident that was thought to have killed him, he was taken in by Madara and brought back to health. This in itself didn’t turn him bad, as he had just renewed his faith in himself and forged a true friendship with Kakashi. But, when released back into the world, he witnesses Kakashi killing the girl that he loved, Rin. Of course, not everything was as it seemed, and Madara was fully aware of the true situation. Still, the old Uchiha used that information to twist Obito’s mind, making him the face of the Akatsuki.

He took on the mantle of Tobi and his first major task was to steal the Nine Tail Spirit and destroy the Hidden Leaf. On that night, Naruto became the Nine Tail’s Jinchuriki as his mother, the former Jinchuriki, and his father, the Fourth Hokage, died saving the city. Tobi was plunged deeper into darkness at that point after facing his own teacher, who failed to recognize who Tobi  truly was. 

Tobi and Madara’s Plan

Now that Tobi was swayed to the dark side, it was time for him and Madara to take revenge against the Hidden Leaf for all they had done to the Uchiha clan, and to restore peace to the world. There was a tablet hidden in the Uchiha’s part of the village that told of how to save the world and how the Uchiha clan was needed to do so.

Madara had long ago determined what the Gedo Statue truly was. It was the husk of the Ten Tails, the first Tailed Beast to ever exist. Its power and ferocity had to be quelled, so it was split up into the nine Tailed Beasts that the world now knew and its body was sealed away. By stealing all of the beasts back, they would be able to revive the Ten Tails, and thus the Akatsuki was born.

With the Ten Tails, a new Jinchuriki could be made, one more powerful than what the world had ever seen. That Jinchuriki would be able to bring peace to the world thanks to a technique known as the Infinite Tsukuyomi.

Infinite Tsukuyomi

This is something you’ll hear mentioned quite a bit, especially when you start to near the end of Shippuden. The Infinite Tsukutomi is why the Gedo Statue has been fed the Tailed Beast Spirits to release the Ten Tails in the first place. It is a genjutsu that Madara Uchiha plans to use to enslave the entire world in order to build the perfect shinobi utopia.

Using the moon, a Rinne Sharingan is reflected across the world, locking everyone in a dream state that is controlled by the one who casts it. The original plan was for Obito to re-create the God Tree in order to cast the genjutsu, but when that plan is foiled, Madara uses his very own Rinne Sharingan to do the deed.

Luckily, there are a few individuals who find themselves immune to the Infinite Tsukuyomi’s effects. These include Kekashi, Naruto, and Sasuke who must fight to end the dream. In fact, it takes the power of the Nine Tails (Naruto) and a Rinnegan use (Sasuke) to stop the Infinite Tsukuyomi, so there’s no surprise that those two managed to avoid its effects. It is no easy task, though, as they must both agree and strategize. 

The Sage of the Six Paths and His Sons

This is where Naruto gets a bit weird. The Sage of the Six Paths is considered the greatest Shinobi of all times; he was the founder of Ninshu (the religion that lead to ninjutsu), and he is why the Tailed Beasts exist in the way they do now after he split up his own Ten Tails to form them. From the sage, whose name was Hagoromo Otsutsuki, was born the Senju and Uchiha clans, although not directly.

Indra, his older son, was powerful and a master of his skills, and he would eventually sire children who would become the Uchiha Clan. Asura on the other hand was weaker, but had more heart, which led him to greater power, and from him the Senju clan would prosper. Hagoromo felt like his younger son followed the correct path, and so he chose Asura as his successor. This started a war that would continue on for generations.

It turned out that the spirits of both Indra and Asura are reborn inside of others, leading to war until they can finally find peace. Both Madara and Hashirama were descendants, and since they could not find peace, they too continued the endless war. But Naruto and Sasuke also have the spirits, and it was not by chance but by fate that they ended up on divergent paths. However, it was up to them to finally reconcile the rift between the two and find peace.

The Sage of the Six Paths appears to both Naruto and Sasuke, telling them of the history of their bloodlines and giving them the power to change destiny, yet they still had to choose to change it. With the Infinite Tsukuyomi in effect and another big threat on the way, they were going to have to make a choice quickly. 

Kaguya Otsutsuki

After being empowered by Hagoromo Otsutsuki, both Naruto and Sasuke now had to face someone even more powerful, the Sage of the Six Path’s mother. When Madara became the ten-tails Jinchuriki, he was actually following a plan laid out by the deceased princess long ago. The tablet that Madara had been following, the one that led him down this path, was altered by Black Zetsu, the living will of Kaguya. It was a plan to bring her back to the world of the living.

Kaguya is the mother of the Sage of the Six Paths, and is responsible for the Chakra that is now prevalent in all shinobi after eating the fruit of the God Tree. She came from the stars, and was treated as a goddess as her power overwhelmed all in her wake. She was also the original Ten Tails Jinchuriki.

Using Madara as a sacrifice, she returns to the world only to take it over. Madara’s Infinite Tsukuyomi has everyone in a slumber, and only a few stand in her way. Both Naruto and Sasuke must defeat her, the same way her son, the Sage of the Six Paths, did many years before. She is no easy target, though.

Thanks to her special bond with chakra, she can use all forms of nature, manipulate time and space, and even turn her body into a weapon. She possesses multiple Kekkei Genkai, making her almost impossible to approach, and her murderous spirit is not to be trifled with. She also has incredible healing abilities, rendering her almost unkillable.

The sad part is that she truly wanted peace, but she was using a horrible means to attain it. By controlling everyone with a genjutsu, it was a false peace, devoid of choice and free will. Naruto, one to always care about others, hated her plan and knew she must be stopped no matter how good her intentions were.

Sasuke and Naruto do manage to triumph over her after a long, drawn out battle with the help of Sakura Hurano, the final member of Team 7. 

Naruto vs Sasuke

After defeating Kaguya, Sasuke finally makes his decision on what he wants to do with his life. He wants to seal all of the Tailed Beasts and become the leader of the Hidden Leaf, even if that means killing Naruto to do it. The final battle between the outcasts who became brothers begins.

Throughout the series, Naruto was always faced with decisions. Does he continue to try to save a person who refuses to be saved, or does he put him down for good? Even though he has nothing but love for Sasuke, Naruto resigns himself to killing his friend. Naturally, things aren’t that easy.

Sasuke, hellbent on making the past right, will continue on in Indra’s footsteps. The two meet at the Valley of the End, where the statues of Hashirama and Madara stand for their final bout. After a long battle, where they both give their all, they are left dying on the ground. Both of them have lost an arm as their ultimate attacks collide. It is in this moment that the curse is lifted. They see that they need each other, and that together they can accomplish their dreams. Sasuke, doing what he can from the darkness, and Naruto taking his spot in the light after being shunned for so long.

As they finally embrace their bright futures, Naruto Shippuden nears its end. 

The Seventh Hokage

After years of turmoil and being considered an outcast, Naruto has finally achieved his dream. He has become Hokage of the Hidden Leaf and leads his village with power and love. Sasuke plays an important part in the village as well, protecting it from any who would do it harm. The spirits of Indra and Asura work in unison now as these two powerful shinobi have accepted one another.

Much has changed since the battle with Kaguya. Everyone is married, yes, even Naruto. It turns out that Hinata really did love Naruto and he realized that he loved her too. Before he becomes hokage they marry and their children are now paving the way for Shinobi in the future. The threat of war is still far from dead as everyone continues to push for peace. Who knows what adventures the future may hold for the man who was once just that little boy with a deadly spirit.

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