Mods for Doom 3 and Resurrection of Evil are almost always distributed as their own PK4 files. You install them by placing these modded .pk4 files into the correct game folder.
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Disclaimer: Ensure all downloaded PK4 files are obtained from reputable sources to avoid malware. Key Takeaways are archives containing game assets. d3xp is the directory for RoE files. Missing pak000.pk4 is the most common cause of failures. Verify game files via Steam/GOG to fix corrupt downloads. Mods for Doom 3 and Resurrection of Evil