The Conspiracy is a group of corrupt and evil adults that secretly controls Tokyo through the use of the Metaverse for their twisted desires. The Phantom Thieves of Hearts fight against their corruption by stealing their Treasure in order to reform them. Once the Phantom Thieves become famous, the Conspiracy decides to hunt them down and kill them. Their ultimate goal is to have Masayoshi Shido elected Prime Minister and implement his self-centered political beliefs, which would give them legal authority to remove any opposition to their desires.
In order to achieve their goals, the Conspiracy has a mysterious black masked assassin (later revealed to be Goro Akechi) trigger mental shutdowns and psychotic breakdowns to specific targets in order to discredit the current government administration and call for a general election, while Shido increases his personal popularity by calling out the government's supposed incompetence and promises to create a greater Japan for all of its citizens. Members who know too much and pose a danger are executed by Akechi, who murders Shujin Academy's Principal Kobayakawa, the Director of Special Investigations Unit, and Kunikazu Okumura when they no longer serve a purpose as members.
While Kobayakawa became an enemy of the thieves after their first heist created a cloud of scandal over the school, the group itself becomes hostile after Junya Kaneshiro is arrested, as he was a primary financial backer of the group and his confession deeply hurt the group's bottom line and resource base. Initially, a tech firm CEO poses as the online hacker activist group Medjed to threaten the Phantom Thieves into compliance (although the ultimate plan was to lose anyway to increase the Phantom Thieves' popularity and make them ideal scapegoats), but after Futaba Sakura successfully breaks into his server and defangs him, they decide to try a subtler approach, kicking a heist request on Kunikazu Okumura to the top of the list artificially, as they had planned to assassinate him; after the Thieves steal his Treasure, Akechi kills Okumura's Shadow Self and Okumura dies during a live press conference, causing the public to believe the Thieves were responsible for his death. Akechi also plants a false calling card in Kobayakawa's office, leading the police to conclude that the Phantom Thieves are responsible for the mental shutdown incidents and leading to the launch of a full investigation.
Lesser members of the Conspiracy appear as Cognitive existence in Shido's Palace, but Shido's personality is so strong that many of them turn out to be actual Shadow Selves who did not form Palaces of their own. After Shido is defeated and experiences a change of heart, the Conspiracy is greatly weakened and rendered impotent politically, but the surviving and unredeemed members retain Akechi's knowledge of the Palace and plan to use it for even more sinister plans like ensuring both the control of Japan and better foreign relations. With the aid of Yaldabaoth, they also manipulate the media to make the public believe that Shido is in poor health and that there is no evidence that the Phantom Thieves actually changed people's hearts. In order to defeat the remaining members of the Conspiracy and reform the whole world, the Phantom Thieves destroy Yaldabaoth, causing the collapse of Mementos and the entire Metaverse, preventing anyone from ever taking advantage of the Palaces and dissolving the Conspiracy once and for all.
- Yaldabaoth: Conductor
- Masayoshi Shido: Leader (Samael)
- Goro Akechi: Assassin
- Junya Kaneshiro: Financier (Bael)
- Ichiryusai Madarame: Financier (Azazel)
- Kunikazu Okumura (Mammon)
- Principal Kobayakawa
- SIU Director
- Yakuza cleaner (Ongyo-Ki)
- IT Company President (Oberon)
- TV Station President (Hanuman)
- Former Noble (Forneus)
- Politician Ooe (Yamato-no Orochi)
- Real versions of the guests in Shido's Palace
- Proxy SIU Director: Successor the previous Director.
Some unconfirmed possible members include Suguru Kamoshida (given Kobayakawa's knowing allowance of his behavior, it is possible that Kamoshida has some hand in the conspiracy).