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Why was the Japan Defense Agency upgraded to the Ministry of Defense?
Literal
Defense-Agency [subject-が] Defense-Ministry [into-に] was-upgraded [nominalizer-の] [topic-は] why is [question-か]?
A political/administrative question. 格上げする ('to upgrade in rank/status,' 'to promote,' 'to elevate') is a compound verb: 格 (rank, status) + 上げる (raise) = 'raise in rank.' Its passive 格上げされる ('be upgraded') is the common form for institutional promotions. The historical event: in 2007, the 防衛庁 (Japan Defense Agency) was officially elevated to the 防衛省 (Japanese Ministry of Defense), changing its rank from an agency (庁) to a full ministry (省). A cleft construction frames the 'why': 'as for the fact that X was upgraded, why is that?'