Copy base/pak000.pk4 to pak004.pk4 (from the install CDs/DVD)
and  base/pak005.pk4 to pak008.pk4 (from patch 1.3.1) here.
(Or pak000.pk4 to pak008.pk4 from your Doom3 Steam version)

(Or copy dhewm3.exe and all the DLLs from the parent folder to your existing,
patched Doom3 installation)

See https://github.com/dhewm/dhewm3/wiki/FAQ#which-game-data-files-are-required
for more details.

The md5sums and sizes of those files are:
pak000.pk4 : 71b8d37b2444d3d86a36fd61783844fe 337MB
pak001.pk4 : 4bc4f3ba04ec2b4f4837be40e840a3c1 220MB
pak002.pk4 : fa84069e9642ad9aa4b49624150cc345 398MB
pak003.pk4 : f22d8464997924e4913e467e7d62d5fe 303MB
pak004.pk4 : 38561a3c73f93f2e6fd31abf1d4e9102 227MB
pak005.pk4 : 2afd4ece27d36393b7538d55a345b90d 540KB
pak006.pk4 : a6e7003fa9dcc75073dc02b56399b370 214KB
pak007.pk4 : 6319f086f930ec1618ab09b4c20c268c 118KB
pak008.pk4 : 28750b7841de9453eb335bad6841a2a5  12KB
