K1n9_Duk3's Patching Utility is a 32-bit Windows program (commonly referred to as Win32). You need to run it on a 32-bit or a 64-bit version of Windows. I have only tested it on Windows XP (32-bit) and Windows 10 (64-bit), but I think it's gonna work on any version of Windows XP and up. It may also work on Windows NT, 95, 98, ME or 2000 if you have Unicode support installed on that system (I haven't tested this myself). Linux users might also get it to work through WINE.
You should run the patching utility on a (semi-)modern PC to patch the executables and then copy the patched files over to your DOS PC.
The correct procedure is:
- copy the patching utility (KDPU.EXE) onto your Windows PC
- copy the patch script into Notepad
- save the patch script as a plain text file
- open that file in KDPU
- point KDPU to the executables and, once it is done patching each file, save that file (don't overwrite the original files unless you have backups!)
- copy the patched files onto your DOS system along with all the other game files
- run the patched executables to play the game
The original executables for Secret Agent are compressed with LZEXE. KDPU will automatically decompress them and save the patched files in uncompressed form. You should be able to tell the originals and the patched ones apart by looking at their file size.