Spoilers for Volume 100’s FBI hunt: the organization’s operation, Camel’s staged death, Rum, and Bourbon’s real allegiance.
Bourbon does not appear as a field operative in The Black Organization’s Scheme, and the story does not explicitly explain why. His usual work as an investigator makes a separate assignment plausible. It does not prove where he was, what he knew, or whether he contributed behind the scenes.
The absence stands out because so many major members are involved while Andre Camel and the FBI face a desperate situation. Amuro’s position as an undercover Public Security Bureau agent makes it tempting to fill that gap with either a secret rescue or a hidden betrayal. Neither has been established in this account.
What is actually shown during the hunt?

The manga story runs through Files 1061-1066, Volume 100, chapters 3-8. Its anime adaptation is Episodes 1135-1137 (Japanese episodes 1077-1079): The Black Organization’s Scheme (Hunt), The Black Organization’s Scheme (Landing), and The Black Organization’s Scheme (Identity).
Gin, Vodka, Vermouth, Kir, Chianti, Korn, and Rum are involved. The organization reads the FBI’s movements and uses that advantage to pursue its agents. Conan and Akai work to keep Camel alive while preserving the impression that the organization’s attack succeeded.
Bourbon is not shown among the field participants. That is a statement about what the story depicts, not proof that he had no knowledge of the operation. The reverse is equally important: the fact that he could have known something is not evidence that he did.
Why his absence feels so conspicuous
Amuro occupies several roles at once: Café Poirot employee, private detective, organization operative Bourbon, and Public Security Bureau officer Rei Furuya. In a confrontation with the FBI, more than one of those roles could matter.
Kir’s presence shows how tense it can be for an infiltrator to stand inside an organization operation against other investigators. Amuro’s absence leaves that tension unresolved in a different way. We cannot see which demands on his position, if any, govern his behavior here.
The uncertainty belongs to the story. It is the reason to examine possibilities, rather than an invitation to assign him a role that has not been shown.
Three possible explanations and their limits

A different kind of assignment
The most straightforward theory is a division of work. Gin’s team is engaged in direct pursuit and elimination, with Vodka assisting and Chianti and Korn providing sniper fire. Bourbon often works by approaching a target, testing an identity, and drawing out information.
His investigation of Akai’s fate and his assignment concerning Shinichi Kudo fit that pattern. A separate intelligence task would therefore be consistent with how he usually operates.
It is still a theory. The distinction does not mean Bourbon is incapable of violence or forbidden from field operations, and this episode does not show an order excluding him. Different roles make the absence understandable without proving its cause.

Protecting his cover under Rum
Rum gives Bourbon instructions to investigate Shinichi. As an infiltrator taking orders within the organization, Amuro risks exposure if he openly favors an opposing agency.
That danger could limit his freedom to intervene. But the story does not state that Rum suspected him, blocked him from joining this operation, or caught him trying to help the FBI. A general risk attached to his cover is not a revealed explanation for this particular absence.
It is possible to read the situation as a painful limit on an ally’s ability to act. Even then, we do not know whether Amuro wanted to intervene, lacked the information, or had other constraints. The feeling is persuasive precisely because his divided position is established; the specific motive remains missing.

Intelligence work behind the scenes
Because the FBI’s communications and movements are being read, codebreaking or intelligence gathering is another plausible area in which Bourbon might have contributed. Those tasks resemble his strengths.
There is no depicted confirmation that he decoded the FBI’s messages or supplied the decisive information. Rum’s intelligence and the organization’s wider network already matter to the operation. Assigning their success to Bourbon would replace the visible story with an unshown explanation.
The distinction is simple: his ability makes a contribution conceivable, not established. An absent specialist is not automatically the author of every result in his area of expertise.
Did he warn Akai or the FBI?

There is no confirmed advance warning from Bourbon in the events considered here. The heavy losses and desperate response make a full, timely warning seem unlikely, but they do not prove that no limited contact of any kind occurred.
The FBI could have lacked information because Amuro did not possess it, could not pass it on, or was not sharing it. The episode does not choose among those possibilities. It certainly does not establish that he deliberately allowed the attacks out of indifference.
The Public Security Bureau and the FBI have a common enemy, but that does not make their information identical or their working relationship unconditional. Amuro and Akai also carry personal history that cannot be assumed to vanish whenever cooperation would be useful.
What about the tea meeting?
The meeting at the Kudo Residence after the cocktail storyline is an important point of contact involving Amuro, Akai, and Yusaku. It is not, by itself, proof that they agreed to share every subsequent operation.
The details and extent of any arrangement are not established by Bourbon’s absence from the FBI hunt. The later crisis can suggest limits to effective information sharing, but it cannot tell us everything discussed at that earlier meeting.
That leaves a more interesting relationship than either complete reconciliation or total hostility. They may find reasons to cooperate without losing their institutional obligations, private judgments, or reasons to withhold information.

Bourbon’s absence remains unresolved. Separate duties and the restrictions of undercover work are plausible explanations; codebreaking support or a warning to the FBI remain unconfirmed. The episode’s tension comes partly from that gap: a potentially valuable ally exists, yet the people under attack cannot be shown relying on him.
Further reading (contains spoilers): why Akai and Amuro clash.

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