Kakashi's Anbu Arc: The Shinobi That Lives In The Darkness
[ranking: 12]
Kakashi's Anbu arc may be filler, but it answers several questions the original manga does not. It goes into detail about Kakashi, Yamato, and Itachi's time in Anbu. This provides insight into the inner workings of Anbu and also into each character's past.
Viewers learn Yamato, who is a largely mysterious figure, was once a member of Root and Kakashi's enemy. It also digs into how the city handled the Uchiha massacre after it happened and reveals Itachi had been allowed to periodically come back and check on his brother in secret.
The Tale Of Jiraiya The Gallant
[ranking: 3]
Aside from having an amazing name, the Tale of Jiraiya the Gallant is also one of the more touching arcs in the series. Prior to this arc, Jiraiya wasn't a very well-developed character. His primary attribute was being a pervert - a controversial trait that appeals to some viewers, but not others.
This arc turns him into a finely developed, memorable character by further developing his mentor relationship with Naruto and taking a deep dive into his past. It depicts the time he raised three orphans for months on end, training them to defend themselves in a war zone before returning home to Konoha.
The arc shows both his kindness and the consequences of not doing enough. Jiraiya eventually has to leave those orphans, and their subsequent suffering turns them into enemies of Konoha in a later arc. Furthermore, this arc includes Jiraiya's death; not a happy moment, but one of the most emotionally wrenching ones.
The Akatsuki Suppression Mission
[ranking: 5]
The Akatsuki Suppression Mission arc focuses on two members of the Akatsuki, Hidan and Kakuzu, and the fight to defeat them. When Team 10 attempts to take them out, Asuma ends up dying in the process. While this doesn't come as a total shock thanks to the episode's spoilerific title, "Asuma Dies," it still packs a punch.
In what follows, Asuma's loved ones mourn his death, and Team 10 fights to get revenge. Using a plan designed by Shikamaru, the three ninja track down Hidan and brutally murder him for what he did to their teacher. It's one of the most cathartic moments in the series.
The Sasuke Recovery Mission
[ranking: 8]
Throughout the series, one of Naruto's driving forces is his desire to rescue Sasuke Uchiha from himself. The Sasuke Recovery Mission arc is where that motive first develops.
Before Sasuke left Konoha, Naruto viewed him as a rival, though also as a friend. In this arc, Sasuke agrees to receive training from Orochimaru, who offers assistance assuming he'll eventually kill Sasuke and transfer his own consciousness into the boy's body.
Naruto and his fellow ninja attempt to bring Sasuke back to the village, but utterly fail at doing so. Not only is this failure emotionally devastating, it also proves this is a show where the heroes don't always succeed.
The Search For Tsunade Arc
[ranking: 13]
The Search for Tsunade arc is exactly what it says on the tin - a new Hokage is required, so Naruto and Jiraiya are tasked with tracking down Tsunade, the best candidate for the job. This arc sees Naruto's first experiences training under Jiraiya, as well as a spectacular face-off between the Legendary Sannin.
It also introduces the Akatsuki, an organization that has connections to nearly all the serious threats that appear in the anime. Seeing Itachi interact with Sasuke for the first time is painful and makes it easier to sympathize with Sasuke's desire to destroy his brother. Upon a rewatch, it's heartbreaking to see Itachi put on an act of cruelty when all he wants is to protect his brother.
Kakashi Gaiden
[ranking: 7]
Kakashi Gaiden is the arc where viewers get to learn what Kakashi meant when he told Sasuke everyone he cared about had already died.
In this arc, Kakashi's teammate Obito is crushed under a rock and gives Kakashi his sharingan eye under the assumption he'll soon be dead. However, Obito ends up being rescued and nursed back to health by his ancestor Madara, who uses the opportunity to try to recruit him to his cause, which involves destroying and resetting humanity.
Madara succeeds in the cruelest way possible - he forces Obito to helplessly watch as Kakashi kills Rin, Obito's former teammate and first love. Seeing an ancient villain manipulate a little boy and indirectly murder a little girl is harrowing, but it sheds light on the villain's motivations, the brutality of the anime's world, and Kakashi's tragic personal history.
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