The Defense Acquisition Guidebook section 126.96.36.199 Modular Contracting states: "The PM should use modular contracting, as described in FAR Section 39.103, for major IT acquisitions, to the extent practicable."
In the Information Technology Management Reform Act (Clinger Cohen Act) SUBTITLE E--NATIONAL SECURITY SYSTEMS SEC. 5141. APPLICABILITY TO NATIONAL SECURITY SYSTEMS states "Except as provided in subsection (b), this title does not apply to national security systems." Since Modular Contracting in Clinger Cohen (Sect 5202) is not one of the excepted subsections (i.e. modular contracting does not apply to National Security Systems) it seems to me that the appropriate entry to address Modular Contracting in the Acquisition Strategy (MS C) for an air launched missile which is a National Security System would be "not applicable".
Here is so information to help understand the historical background. First, Section 5202 of the Information Technology Management Reform Act (Clinger-Cohen Act) directs federal agencies to use modular contracting "to the maximum extent practical" in the acquisition of major IT systems. Following Clinger-Cohen, the President issued Executive Order No. 13011, which instructs agencies to apply modular contracting "where appropriate" and "to the maximum extent practicable." Second, Section 5141 exempts national security systems from many of the provisions of the act. Finally, the expanded Executive Order 13011 requires other program managers to consider if the modular approach is advantageous to their program.
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You stated that your program is an ACAT 1C and not an IAM or IAC, which would reduce the probably of modular contracting applying. Additionally, you said that your program falls under the National Security System exception, which would further reduce the probability of modular contracting applying. Based on the limited information you presented, there is a low probability that you need to use modular contracting. However, you must ensure that there isn't a large software effort embedded in your program that would otherwise qualify as an MAIS. You must also ensure compliance with the other provisions of Clinger-Cohen in Section 5141.