This paper, the second of three, takes a systems biology view of the bacterial flagellum. The flagellum is the organelle imparting motility to common bacteria. The first paper was a constructive or top-down view from a systems engineering viewpoint: “An Engineering Perspective on the Bacterial Flagellum, Part 1 – Constructive View”. It detailed the typical environment, the purpose, the required existing and new resources, the necessary functional requirements, various constraints, the control means, and the self-assembly of any kind of bacterial motility organelle. The specification of these requirements was intended to be independent from knowledge about the actual flagellum. A converse approach is detailed in this Part 2. It is an analytical, reductionist, or bottom-up view, which discusses the known 40+ protein components and the observed and inferred structure, control, and assembly of a typical bacterial flagellum. This cellular subsystem is well-researched. Much of that research is reviewed herein. However, the assembly orchestration is illustrated in a form and detail not found elsewhere. Part 3 will compare the two views and will conclude with original observations. Those include an ontology of the exceedingly specific protein binding relationships in the flagellum. The latter observation is new and significant.