The filler episodes and arcs of long-running anime, such as Bleach and Detective Conan (the latter of which passed the 1,000-episode mark in 2021 with the help of hundreds of filler episodes), often get a bad rap. They are derided as uninteresting, not animated or written as well as canon material, and worst of all, a pointless distraction from the more exciting main story.
However, there are many examples of Naruto filler episodes that don't deserve the hate in both the original series and Naruto Shippuden, and plenty of villains to make these anime-only arcs shine. Whether they are devious and sadistic like Mizuki or sympathetic like Guren, they can stand with some of the main series' villains.
Yakumo Kurama
Or, more accurately, Yakumo's id. The short filler arc in which she appears gives some background for Kurenai, one of the Naruto characters who never quite lived up to her potential. Kurenai was once brought in to train Yakumo, who had no ninjutsu or taijutsu capabilities but could produce extremely powerful genjutsu.
When Kurenai gave up on her, she sealed Yakumo's powers to prevent her id — a physical, monstrous presence — from taking over her body. The id breaks the seal and lashes out with illusions powerful enough to cause real-world damage. For instance, in the episode "Kurenai's Decision: Team 8 Left Behind," she is able to make lightning strike the Leaf Village simply by painting a picture of it.
Arashi
In the Land of Rice Fields Investigation arc, while hunting for Sasuke, Naruto and Sakura meet a girl named Sasame. Sasame is looking to save her missing cousin Arashi, who went to Orochimaru in hopes of reviving their clan. But when they discover "Orochimaru" in his hideout, it's revealed that he is really Arashi in disguise.
To restore their clan to its former glory, Arashi has been killing and absorbing his clanmates using the curse mark Orochimaru gave him. Now horrifically transformed, he subjects Naruto and Sakura to a truly brutal fight, but dies when the underground hideout is destroyed. In a final redeeming act, he throws Sasame from the collapsing lair, saving his cousin's life.
Hoki
The Cursed Warrior Extermination arc focuses on the new daimyo of the Land of Birds, Sagi, who is mourning his late father and twin sister. Naruto, Neji, and Tenten's mission is to solve the mystery of the spectral Cursed Warrior terrorizing the territory. They are impeded by Mousou, the daimyo's advisor, who attempts to frame an innocent man for the attacks and have Naruto executed for investigating in the palace.
Mousou's true identity is Hoki, leader of the Watari group of rogue ninja. He used genjutsu to fake having powers to earn a place next to the former daimyo, and then murdered him and one of his children in order to take over the country. The climactic battle between him and Naruto pits each shinobi's trademark clone techniques against one another.
Mizuki
Technically, Mizuki was the very first villain Naruto ever encountered. After being imprisoned for trying to steal village secrets and murder Iruka and Naruto in the process, he spent his time working out and nursing a grudge. In the episode "The Three Villains from the Maximum Security Prison," he breaks out to take revenge.
Despite his massive ego, Mizuki proves to be even less of a match for Naruto now that the boy is trained and experienced as a ninja. He takes a drug given to him by Orochimaru that mutates him into a hulking, tiger-like monster, but though the drug maximizes his physical strength, it makes him painfully slow, allowing Naruto and Iruka to take him down with a combo attack.
Mecha-Naruto
While he doesn't have quite the same abilities of Mechagodzilla in Godzilla vs. Kong, Naruto does indeed have to fight a robotic duplicate of himself in the episode "Naruto vs. Mecha-Naruto." An experiment of Orochimaru's accidentally given sentience by a stray lightning bolt, Mecha-Naruto hunts the real Naruto down in order to steal the Nine-Tailed Fox's chakra.
Naruto tries to fend off Mecha-Naruto as it bears down on the Leaf Village, but even with his friends' help, the robot is unstoppable. It nearly drains all of the Nine-Tails' chakra from Naruto, but after its programming is altered, it decides to befriend him instead. It armors Naruto with its own body, just in time to help him fight Orochimaru's other new experiment: Mecha-Nine-Tails.
Kazuma
In the Twelve Guardian Ninja arc, Naruto befriends a young monk named Sora who is also hated by his people because of a destructive power inside him. Sora wants to avenge his murdered father Kazuma. He trains with the Leaf Village ninja and helps them fight the team of rogue ninja attacking the Fire Temple, led by the mysterious Furido.
It turns out that Furido is really Kazuma, believed killed after trying to assassinate the Fire Daimyo. He wants to destroy the Leaf Village to unite the Land of Fire under one king. He is willing to do anything to achieve this, including kill his old comrades and implant remnants of the Nine-Tails' chakra into his own son to turn him into a weapon, technically including Sora on the list of jinchuuriki in Naruto.
Raiga and Ranmaru
As a former member of the Seven Swordsmen of the Mist and the Anbu Black Ops, Raiga is intimidating enough on his own. He and the crime family he assembled take over the Katabami Gold Mine, and controls its people by burying alive anyone who objects to them. Raiga gets wildly excited whenever he gets to hold these "funerals."
However, the source of Raiga's genjutsu is really Ranmaru, a frail boy that Raiga carries around on his back. Ranmaru uses his extrasensory visual jutsu to aid Raiga, and Raiga protects Ranmaru and shows him the outside world. They're no Zabuza and Haku, but they are a powerful duo who legitimately care for each other.
Akahoshi
The Hidden Star Village was formed around a radioactive meteorite. With a special training method, shinobi can harness its power to enhance their chakra, but at the cost of dying from radiation poisoning. The method was outlawed, but upon becoming Hoshikage, Akahoshi made it mandatory for the village's youth.
Fueled entirely by arrogance and greed, Akahoshi doesn't care how many of his people have to die if there's a chance to become superior to the five main villages. He murders several himself, including the previous Hoshikage, and when cornered implants the meteorite in his own chest to power up, heedless of the damage it could do.
Aoi Rokusho
In the Land of Tea Escort Mission arc, Team 7 must protect Idate Morino as he competes in a footrace to settle a dispute between rival clans. Shinobi protection is absolutely necessary: Idate's opponents have hired one of the most intelligent Naruto villains, Aoi Rokusho, to murder him. Aoi's stolen weapon, Sword of the Thunder God, is strong enough to overpower even Sasuke's Chidori.
Prideful and sadistic, Aoi is also a very personal villain for Idate: his manipulations were the reason Idate fled the Leaf Village as a child, leaving Idate estranged from his brother Ibiki and with intense shame and trust issues. While trying to kill Idate, Aoi taunts him relentlessly about how he once trusted him, and how afraid Idate still is of him.
Guren
Naruto is well known for its sympathetic and even tragic villains, so even its filler characters get several emotional moments in. Guren is fiercely loyal to Orochimaru, one of the most evil Naruto villains, to the point that she killed a woman who had helped her because her master ordered it. To her horror, she was too late to become his next vessel, and was assigned to escort a boy named Yuukimaru to him for use in his experiments instead.
Despite being happily ruthless in battle, Guren comes to care for Yuukimaru and want to protect him. Especially after she learns the woman she killed was his mother, she is willing to turn on Orochimaru for his sake. Using her incredibly powerful crystallization jutsu, she freezes herself and a reanimated Rinji into crystals to keep him from harming Yuukimaru. She is later saved by Gozu, but her devotion is proven.