Team Rocket was an extremely dangerous organization in Pokémon led by Giovanni. It was best known for being behind the creation of Mewtwo, trying to take over the world through various efforts including stealing Pokémon, and having (at least a few) capable minions including Domino, Butch, and Cassidy.
However, there are plenty of villainous organizations that are far more dangerous than Team Rocket. From the Black Swan Collective conducting illegal experiments to speed up human evolution to Ouroboros collaborating with Apollon Media to gain business for their many minions, these villainous organizations are effective and deadly with their work, achieving their goals with little-to-no opposition.
10 The Black Swan Collective Conducted Illegal Experiments To Advance Human Evolution (Mr. Love: Queen's Choice)
The Black Swan Collective from the romance anime Mr. Love: Queen's Choice appeared to be a gene research institute on the outside, but the reality of this organization is much darker. Masquerading as a gene research institute gave them the ability and equipment to conduct illegal, dangerous experiments to advance human evolution for their own twisted ends. Since the main heroine had an alter ego named Queen that could power up anyone else's EVOL abilities, they pursued the heroine to awaken her alter ego for their own purposes. Hades was a prominent member of this organization and also the final villain in the anime adaptation.
9 The Phantom Troupe Killed The Kurta Clan &Caused A Massacre At The Underground Auction (Hunter X Hunter)
The Phantom Troupe was an infamous band of thieves with Class-A bounties, with most of the members originating from Meteor City. Led by Chrollo Lucifer, these thieves worked together as a group to pull off heists, including killing the Kurta Clan for their scarlet eyes and massacring the attendees of the Underground Auction to steal all of the items available during the Yorknew City arc. However, Kurapika stabbed Chrollo with his Judgement Chain so he would be unable to use Nen without dying in the process. This forced the Troupe to find ways to restore Chrollo so he could use Nen without dying.
8 The Noah's Ark Circus Kidnapped Children For Father's Own Purposes (Black Butler: Book Of Circus)
Noah's Ark Circus was mainly led by Joker, but each of the members knew that Father was the true person behind their formation. Wherever this fun-looking circus troupe went, children went missing, and this forced Queen Victoria to make Ciel and Sebastian investigate the circus undercover.
It was later revealed that Father's true identity was Baron Kelvin, who grew obsessed with Ciel from the moment he met him. He also used the children at Renbourn Workhouse as hostages to make sure that Joker and the rest of the circus would continue obeying him. Though he first assumed Ciel was dead after finding out that he would be used as a sacrifice, he eventually found out that Ciel was still alive and had the troupe kidnap children to lure Ciel out for himself.
7 The Akatsuki Were Once Good But Turned Evil (Naruto)
The Akatsuki was a group of shinobi existing outside the system of hidden villages. The group was originally founded to bring peace and justice to their world at the time, but the next leader, Nagato, came to believe that the world could only find peace if it was exposed to enough traumatic and catastrophic destruction so that the inhabitants would never cause any harm again. They began to make the world dependent on their group by hiring themselves out as assassins and put all of the other shinobi groups out of business to do so. These activities continued with later leaders up until the final leader, Shin, was betrayed and killed by clones of himself.
6 The Twelve Demon Moons Are The Most Powerful Demons To Exist Other Than The King (Demon Slayer)
The Twelve Demon Moons, also known as the Twelve Kizuki, was an organization made of the twelve most powerful Demons in existence and were led by Muzan Kubutsuji, the Demon King.
The group is divided into two ranks: the Upper Ranks, numbered one through six, and the Lower Ranks, also numbered one through six. The smaller the number, the more powerful each member is. Their missions mainly consist of destroying the Demon Slayer Corps and finding the Blue Spider Lily. Upon finding out that Nezuko is sun-proof despite being a demon, Muzan also ordered the group to capture her and bring her to him.
5 The Homunculi Served The Treacherous Father's Plans (Fullmetal Alchemist)
The Homunculi served Father in Fullmetal Alchemist as his main force. Each of its members is named after the seven deadly sins, Lust, Greed, Gluttony, Wrath, Pride, Sloth, and Envy. Each of the Homunculi was created when they broke off from Father's own Philosopher's stone and fused with the body of a living being. They are extremely dangerous, as each of them has their own special powers to instantly destroy any normal person, but they can be killed off permanently after their Philosopher's stones run out of regenerative power.
4 The Red Dragon Crime Syndicate Was Involved In Several Exploits & Feuded With Another Crime Syndicate (Cowboy Bebop)
The Red Dragon Crime Syndicate was a structured crime organization based in Tharsis and located on Mars. Members could only leave the organization once they died, leading former members, including Spike Spiegel, to fake their deaths to actually leave alive. The organization had several exploits, including the Red Eye trade, but they got into trouble with the White Tiger Crime Syndicate from 2065 onward. Both organizations attempted to sign a truce in 2071, but it failed after Vicious, one of the Red Dragon Crime Syndicate members, murdered fellow member Mao and White Tiger's capo Carlos in opposition.
3 Arachnophobia Sought To Become The Leading World Power (Soul Eater)
Arachnophobia was led by the witch Arachne. Their main base of operations was located in South America deep under the Amazon basin, and their main objective was to overthrow Death and make themselves the new masters of the entire world.
The members are also deeply devoted to Arachne and see her as a mother figure, supporting her as she tried to become "The Mother Of All Things." They also have many resources and technology they use for making Demon Tools, as part of their mission to overthrow Death Weapon Meister Academy as the leading world power.
2 The Band Of Seven Were Beheaded But Later Brought Back To Life (Inuyasha)
The Band of Seven, also known as the Shichintai, was made up of seven bloodthirsty mercenaries who enjoyed killing. Their killing spree got so bad that the warring feudal lords at the time banded together to capture and behead them. However, the Band of Seven was later resurrected by Naraku with the Shikon Jewel Shards so they could provide a distraction and defense against his enemies while he took time to recover and separate his heart from his body. Despite being deadly foes, they were eventually defeated and killed by Inuyasha and his allies.
1 Ouroboros Secretly Collaborated With The President & CEO Of Apollon Media, Maverick (Tiger & Bunny)
Twist villain Maverick was revealed late in Tiger & Bunny to be working with the villainous organization Ouroboros, a largely covert terrorist organization. Maverick struck a deal with them to supply villains for the Hero TV show in exchange for access to Barnaby's parents' technology. Members of this organization included Kriem and Jake, and Maverick had a small amount of influence in the organization since he had men dispatched to kill Samantha Taylor. All of Ouroboros' known members also have a tattoo of the organization's logo somewhere on their bodies, except for Maverick since he technically was not part of the organization.