All WolfenDOOM scenarios include a wad file and a deh patch file, and they cannot be run with the regular Doom II engine (doom2.exe). In the past, I recommended three source port engines as the most compatible with WolfenDOOM: Legacy, PrBoom, and MBF. However, I've found that another source port, Risen3D, is now the most stable and best all-around engine for running WolfenDOOM wads. You can download it here.

After you've downloaded Risen3D, be sure to carefully follow its instructions so that you can properly set-up each WolfeDOOM scenario and load each scenario's wad and deh files.

Two WolfenDOOM scenarios include their own engines which should be used to play them instead of using Risen3D or any source port. These are The Original Missions and The Nocturnal Missions. The engines bundled with these two scenarios were coded by Joel Murdoch to emulate the original Wolf3D game as accurately as possible.