The Shinobi Agency （Shinobi機関 Shinobi Institute) is a top secret government agency that conducts underground and often illegal activities using Ninja from various clans for government purposes from demolition, to sabotage, to kidnapping, and assassination. Hotsuma, Jimushi, and Hibana worked for them for a time.
The Shinobi Agency is an organization shrouded in mystery. Under orders of both the old government and the new government in Osaka, the Agency is responsible for covert operations and top secret missions. These missions are handled based on the shinobi's skills, and many of them would range from life threatening to illegal. Agents of the provincial government send a small number of shinobi to act in counter terrorism, guarding of important officials, and take on shinobi missions including assassination. All knowledge of this agency is top secret and is therefore forbidden to be known by the general populace.
Golden Palace Incident
During the opening part of the 21 Century, Hiruko Ubusuna, a heretic sorcerer that was secretly defeated and sealed away by the Oboro Clan, was resurrected and instigated the slaughter of the Oboro and the destruction of Tokyo. Assisted by the Agency, Hotsuma, the leader of the forsaken Oboro Ninja, hunted down and killed Hiruko at the castle keep of the Golden Palace. After his victory, Hotsuma died in the palace's collapse. When the Agency and Kagari Ubusuna went to find him, there was only rubble and the symbol of the Oboro clan's family head, the demon blade Akujiki that were left.
Akujiki Retrieval Mission
After the Ariake Seal collapsed, Hellspawn began reappearing in the city. The Shinobi Agency discovered that it was the theft of the key component of the seal; a shard of Akujiki that led to this debacle. The Agency also confirmed it to be the work of Nakatomi Conglomerate Mercenaries led by Jimushi, a former member of the Agency who deserted after becoming disenchanted with the organization. To counter this, the agency sent Hibana; the last of the Oboro Family and their kunoichi agent to retrieve the sword fragments before Nakatomi does.
Hibana battles through scores of Nakatomi Ninja Mercenaries and cuts through the various Hellspawn that manage to leak into the mortal plane, including Hellspawn created from the rampaging Akujiki's own power. During the conflict she faces her former mentor Jimushi, who tries to give Akujiki to her after attempting to warn her of the Agency and Nakatomi's darker side, only to be murdered by the cyborg ninja Kurohagane who makes off with the other Akujiki pieces. After Hibana slays the final Akujiki Hellspawn in the Golden Palace Ruins, she faces Kurohagane who steals Akujiki's final shard and reforges the blade, transforming into a demonic ninja appearing as a sinister clone of Hotsuma.
After a grueling battle at the top of the palace, Hibana succeeds in defeating the Akujiki enhanced Kurohagane and takes Akujiki fulfilling her mission.
As the sun rises she is ordered by the agency to give Akujiki to the government collectors, but hesitates sensing something foul. Hibana reluctantly gives them the sword but is quick to notice the Nakatomi insignia on the carrying case. As she leaves the area, and overhears the government planning to capture Kurohagane, she makes enough distance and removes the helmet of her shozoku created by the Agency, and is revealed to have switched the true Akujiki with the Utsushiyo blade the Agency itself created. Taking her family inheritance as her own, Hibana leaves the agency as a renegade shinobi, and proceeds onward, her whereabouts a mystery.
- The secret coin used in Kunoichi/Nightshade is the Shinobi Agency insignia; which is a stylized version of the Japanese word "Shin/Kokoro" (心), which is one of the two radicals that make up the Japanese word Shinobi (忍)