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McDaniel envisioned Thrush1 as a hierarchy with only a few levels. A "flat" organizational style, to use a term from books management.
1. As explained in The Dagger Affair, McDaniel treated Thrush as an acronym: The Technical Hierarchy for the Removal of Undesirables and the Subjugation of Humanity. "Undesirables" were, of course, anybody who couldn't or wouldn't work for Thrush, and especially those who actively opposed it. Why did Thrush want to "subjugate" humanity? Because most of those who worked for Thrush, and everybody at the highest levels, wanted power. Power for its own sake, power to accomplisht the things they wanted to achieve.
The Council: sets the goals for the Hierarchy as a whole, and controls projects and operations that require the resources of more than one Satrapy.
The Ultimate Computer2: Designed to work problems in strategy and logistics, decides the best plan of attack and allocation of resources for a given operation. The Ultimate Computer was first mentioned in "The Ultimate Computer Affair," season 2, episode 3.
Satraps: Thrush divides the world into sectors which it calls "satrapies". Each satrapy is run by a "Satrap". Ward Baldwin is the Satrap of the San Francisco Satrapy, which includes not only San Francisco itself, but also Alameda and Contra Costa counties in the East Bay region.
Individual employees, often referred to as "Thrushes" by U.N.C.L.E. agents. When a group of Thrush employees is given a task to do together, there will often be a team leader who will supervise the others, providing on-the-spot leadership while reporting often (or continuously, if the mission is important) to the Satrap. But team leader is not a permanent position, and the selection will often rotate from one thrush to another, depending on the needs of the particular mission.
2. As envisioned by McDaniel, the Ultimate Computer is not one computer but three. It is designed based on a principle now used for computer systems that must be "always on": there must be no single point of failure. The Ultimate Computer faces not only the possibility of hardware and/or software failures, but also attack by a hostile force (U.N.C.L.E.), so its location changes at random intervals to prevent it being captures.
At any given time, one of the three computers is operating and directing global Thrush operations; one is being packed into boxes for transport, or has arrived at a new location and is being unpacked and set up; and one is in transit from one location to another.
As soon as the new computer has been set up (parts connected together, boot up, etc.) it takes a download of the current situation from the operational computer. From that point on, the two computers run in parallel.
If the active computer were captured or destroyed by U.N.C.L.E. or other hostile forces—or a natural disaster—the backup computer could immediately take over, and Thrush would be without overall direction for less than a second. A new computer would then be assembled from parts already stored in various warehouses and would become the one "in transit", while the one currently in transit would become the backup as soon as it arrives and is set up.
Thus, Thrush could continue to operate without interruption unless at least two computers were captured/destroyed within a short time period.