SPLIT FILES is designed for this situation, but it applies the splits within each procedure. So if the report runs multiple procedures for each department, which it seems that it does, and you want the output grouped by department or even in separate output files, SPLIT FILES would leave you with a lot of rearranging to do.
In that case, the SPSSINC SPLIT DATASET and SPSSINC PROCESS FILES extension commands would be appropriate. SPLIT DATASET would make a separate sav file for each department's data, and PROCESS FILES would iterate over those files producing the output for each department either grouped sequentially by department or in separate spv files. The processing could include exporting in whatever final format you need.
These commands can be installed via the Extensions > Extension Hub menu. The first time you use PROCESS FILES, it will take a bit of time to get the hang of it, but it will save you a lot of manual work.
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