The Ministry Intelligence Agency, or MIA for short (known as the MBI, Ministry Bureau of Investigation, in the English version of Yakuza) is an intelligence agency featured as one of the primary antagonistic factions of Yakuza and its Kiwami remake.
According to Makoto Date, the MIA is a branch of the Japanese government's Interior Ministry which answers directly to the Cabinet Office; which is to say, it answers directly to the Japanese Prime Minister. The MIA are tasked with sensitive, confidential matters, ranging from counter-terrorism, to espionage, to the protection of Japanese foreign dignitaries. The MIA operates with extensive powers to serve the Japanese government's interests both in the Japanese mainland and abroad.
Aside from the dubiously ethical nature of its main purpose, the MIA is also a deeply corrupt organization. By the events of Yakuza, its Director, Kyohei Jingu, has essentially turned the MIA into his own personal, government-funded army; with the apparent knowing cooperation of several of its members.
Prior to the events of the game, Director Jingu had made an illicit partnership with the Tojo Clan's Third Chairman, Masaru Sera. Their original deal entailed Jingu helping the Tojo to launder the vast reserves of cash they accumulated in exchange for a cut of the proceeds. However, Jingu betrayed the Tojo and instead appropriated the money for himself, storing it in an account in the Toto Bank which he controlled. Jingu would then use his control over these vast reserves to force Chairman Sera into using the Tojo Clan to serve Jingu's political ambitions.
In 2005, Sera finally had enough of being coerced by Jingu when the MIA Director ordered him to murder his former lover, Yumi Sawamura, and their illicit daughter, Haruka. With help from Yumi and his longtime friend and ally, Shintaro Kazama, Sera robbed Toto Bank and stole back the 10 billion yen reserves which Jingu had stolen from the Tojo.
Jingu became desperate to recover the money, since his future political plans required it. After he discovered Yumi's involvement in the robbery and the fact that a pendant she'd given Haruka was key to finding the money, Jingu sent one of his top operatives to recover the pendant and kidnap Haruka. Unfortunately for him, thanks to Kazuma Kiryu's intervention, the operative failed and ended up being killed by one of his own men to keep him from revealing information to Kiryu.
The MIA would go on to form a partnership with the Nishikiyama Family to recover the money with their support, but Patriarch Akira Nishikiyama would fail to get the pendant from Kiryu. Director Jingu would then move on to align with the Go-Ryu Clan, a subsidiary of the Omi Alliance, offering to give them the money once recovered in exchange for their help in controlling the Tokyo underworld.
After learning that the 10 billion yen was being stored in a hidden vault atop the Millenium Tower, Jingu mobilized along with an entire squadron of elite MIA operatives to take control of the Tower and recover the money. Unfortunately for them, Kazuma Kiryu would once again foil his plans by confronting Jingu at the Millenium Tower's penthouse bar, Ares, and fighting him and all his MIA forces. Much to Jingu's shock, Kiryu single-handedly defeated them all. Soon after, a remorseful Nishikiyama would kill himself with a bomb in order to assassinate Jingu and prevent him from killing Yumi, Kiryu and Haruka.
After Jingu's corruption and the MIA's unscrupulous methods were publicly exposed by Detective Date and Junichi Sudo, the Japanese government shutdown the MIA to try to quell the controversy.