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. If the rigged election went well, the Conspiracy had secretly planned to dispose of Akechi as well, as he would have outlived his usefulness and knew of Shido's dealings.
Before the events of the game, Shido also personally attempted to seize and ruin the lives of cognitive psience researchers. These include Wakaba Isshiki and Takuto Maruki; The former was executed by Akechi per Shido's orders and he ordered an IT company president to encrypt the research without telling him what it actually is, while he seized the research of the latter and forced his university to cut the funds for his lab in Odaiba, with a stadium constructed on it instead. Again, just like the IT company president, after he seized Takuto's research, he gave it to his fellow researchers for analysis without telling them what it actually is for. However, unlike with Wakaba, Shido left Takuto alone without any follow up action, inadvertently allowing him to complete his cognitive research.
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. It was also revealed at this point that despite being a member of the Conspiracy, Akechi is not loyal to them at all and simply worked for both the Conspiracy and the Thieves for his own agenda. Once the Thieves reach Shadow Shido, he reveals that he knows about Akechi's plans to dispose of him and is prepared to dispose Akechi himself if things ever begin to go wrong.
After Shido is defeated and experiences a change of heart, the Conspiracy is greatly weakened and rendered impotent politically. However, Yaldabaoth begins to take action on his own, having seen the protagonist's rehabilitation game complete. He manipulates the remaining members into retaining Akechi's knowledge of the Palace and they plan to use it for even more sinister plans like ensuring both the control of Japan and better foreign relations. In order to make sure their plan ensues smoothly, they also fire Sae Niijima, then 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 public, the Phantom Thieves reach the depths of Mementos, only to find that the "reformed" Conspiracy members are merely made one with the public, and Holy Grail that Yaldabaoth manifests as is indestructible since it feeds on the people's apathy to endlessly regenerate itself. Once the Thieves can no longer fight, it exiles them back into the real world, then merges Mementos with the real world and further manipulates the public to believe that the Phantom Thieves don't exist, causing all of them to be exiled from reality as well and writhing in pain. Yaldabaoth now reveals himself to be impersonating Igor and to have been compromised the Velvet Room and transformed it into a prison where all of the Thieves are imprisoned in after they were exiled by him. The so-called "conspiracy" is now revealed to be rigged by Yaldabaoth to see that if the protagonist's desire for change or Akechi's desire for destruction is stronger, as he deliberately arranges the most foolish and corrupt of people into power for the protagonist or Akechi to take down. Regardless of whoever wins by dismantling the conspiracy, Yaldabaoth will enact his plan to make the public "distorted masses" who only desire safety and stagnation, so he can prove that there will be no more corrupt and foolish conspiracies like those once he rules over humanity. It is heavily implied that even if the conspiracy ever won, the results are the same.
Once this is found out, the Thieves return to Shibuya to climb the Qliphoth World, successfully destroying Yaldabaoth and causing the collapse of Mementos alongside the entire Metaverse, preventing anyone from taking advantage of it and the Palaces anymore. Due to the source of all distortions being removed, people's opinion of Shido changed to an unanimously negative light and thus 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.
- A Psychologist
- Shido-leaning Legislator.
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).
- The Conspiracy is comparable to the New World Order from Persona 2: Eternal Punishment. Both have members in the government, police and entertainment circles, are backed by the Mafia, and are ultimately working for a malevolent deity.
- However, while both are villainous social orders, their goals are completely different; The New World Order attempts to use false mysticism and prophecy to create a delusional utopia where only they live, while the Conspiracy is a more realistic portrait of a corrupt social system, whose sole purpose is to put a corrupt politician into power and remove all opposition.
- The Conspiracy is likely based on a corrupt modern government system or a coterie based on a corrupt politician (In this case being Shido), especially the ones seen in modern Japan. The actions carried out by the members of the Conspiracy, such as blackmailing and assassinating opposition, holding extremist views and trying to achieve ruling status regardless of means, plagiarizing the works of others and abusing workers are in fact, not uncommon in real life political, cooperate and entertainment circles.