Does the DoD Instruction 5000.02 (and subordinate acquisition policy, such as the EVMIG) apply to DARPA? Is DARPA exempt from these acquisition policies somehow (e.g., because it is governed by Intelligence Community acquisition guidance)? The DoDI 5000.02 "Applicability and Scope" section on the cover page offers conflicting guidance -- it says that the instruction applies to all DoD Components, but it also offers an exemption for wholly or majority-National Intelligence funded programs.
In general terms, most of DARPA's activities are not be governed by DoDI 5000.02. For example, there are seven budget activities (BA) or categories associated with Research, Development, Test, and Evaluation (RDT&E) funding. The first three BAs--basic research, applied research, and advanced technology development--are not normally associated with formal acquisition programs and comprise the vast majority of DARPA funding.
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The next four BAs--Advanced Component Development and prototypes, Systems Development and Demonstration, RDT&E management support, and Operational systems development--are an integral part of the acquisition program and are governed by the DODI 5000 series. In practical terms, DARPA takes technology from concept development to technology demonstration covered by BA3 funding. Anything beyond tech demonstration such as prototyping or system demonstration is governed by DoDI 5000.02 unless a wavier has been granted.