"Fixed" coordinate conversion from Quake to Unity, by swizzling Y and Z coordinates during vector conversion. There seems to be a lot of confusion and disagreement about Quake's coordinate system, but this setup is simple and looks correct both in-game and in-editor, and the world isn't mirrored anymore either.

Assets/Scripts/Data/QExtensions.cs

@@ -30,7 +30,7 @@ public static class QExtensions
         return result;
     }
 
-    public static Vector3 ToVector2(this QVec2 vec)
+    public static Vector2 ToVector2(this QVec2 vec)
     {
         return new Vector2(vec.x, vec.y);
     }
@@ -45,4 +45,9 @@ public static class QExtensions
         byte[] v = triVertex.v;
         return new Vector3(v[0], v[1], v[2]);
     }
+
+    public static Vector3 ToUnity(this Vector3 vec)
+    {
+        return new Vector3(vec.x, vec.z, vec.y);
+    }
 }

Assets/Scripts/Data/QModel.cs

@@ -259,6 +259,7 @@ public struct QSurface
     public bool cachedDLight;
     public IntPtr samples;  // Pointer to byte
     
+    // This is safe as the Quake engine guarantees this pointer is never null (see: Mod_LoadFaces)
     public QTexInfo TextureInfo => Marshal.PtrToStructure<QTexInfo>(texInfo);
 
     public IEnumerable<QGLPolyVert[]> GetPolygons()
@@ -311,5 +312,6 @@ public struct QTexInfo
     public IntPtr texture;  // Pointer to texture_t
     public int flags;
 
+    // This is safe as the Quake engine guarantees this pointer is never null (see: Mod_LoadTexinfo)
     public QTexture Texture => Marshal.PtrToStructure<QTexture>(texture);
 }

Assets/Scripts/Modules/AliasModel.cs

@@ -220,8 +220,8 @@ public class AliasModel
         
         for (int i = 0; i < numVerts; ++i)
         {
-            vertices[i] = Vector3.Scale(triVerts[i].ToVector3(), scale) + origin;
-            normals[i] = QLightNormals.Get(triVerts[i].lightNormalIndex);
+            vertices[i] = (Vector3.Scale(triVerts[i].ToVector3(), scale) + origin).ToUnity();
+            normals[i] = QLightNormals.Get(triVerts[i].lightNormalIndex).ToUnity();
         }
     }
 
@@ -232,10 +232,9 @@ public class AliasModel
         
         for (int i = 0; i < numTris; ++i)
         {
-            // Quake triangles are wound clockwise, so we reverse them here
-            indices[i * 3 + 0] = (ushort)triangles[i].vertIndex[2];
+            indices[i * 3 + 0] = (ushort)triangles[i].vertIndex[0];
             indices[i * 3 + 1] = (ushort)triangles[i].vertIndex[1];
-            indices[i * 3 + 2] = (ushort)triangles[i].vertIndex[0];
+            indices[i * 3 + 2] = (ushort)triangles[i].vertIndex[2];
         }
     }
 
@@ -295,9 +294,9 @@ public class AliasModel
             
             for (int vertIdx = 0; vertIdx < header.numVerts; ++vertIdx)
             {
-                Vector3 vert = Vector3.Scale(poseVerts[vertIdx].ToVector3(), scale) + origin;
+                Vector3 vert = (Vector3.Scale(poseVerts[vertIdx].ToVector3(), scale) + origin).ToUnity();
                 deltaVertices[vertIdx] = vert - baseVertices[vertIdx];
-                deltaNormals[vertIdx] = QLightNormals.Get(poseVerts[vertIdx].lightNormalIndex) - baseNormals[vertIdx];
+                deltaNormals[vertIdx] = QLightNormals.Get(poseVerts[vertIdx].lightNormalIndex).ToUnity() - baseNormals[vertIdx];
             }
             
             mesh.AddBlendShapeFrame(animName, (float)index / numPoses, deltaVertices, deltaNormals, null);

Assets/Scripts/Modules/BrushModel.cs

@@ -30,17 +30,17 @@ public class BrushModel
 
                 for (int vertIdx = 0; vertIdx < polyVerts.Length; ++vertIdx)
                 {
-                    vertices.Add(polyVerts[vertIdx].position.ToVector3());
+                    vertices.Add(polyVerts[vertIdx].position.ToVector3().ToUnity());
                     textureUVs.Add(polyVerts[vertIdx].textureUV.ToVector2());
                     lightmapUVs.Add(polyVerts[vertIdx].lightmapUV.ToVector2());
                 }
 
-                // Reconstruct triangle fan (in reverse order)
+                // Reconstruct triangle fan
                 for (ushort index = 2; index < polyVerts.Length; ++index)
                 {
-                    indices.Add(index);
-                    indices.Add((ushort)(index - 1));
                     indices.Add(0);
+                    indices.Add((ushort)(index - 1));
+                    indices.Add(index);
                 }
                 
                 Mesh mesh = new Mesh();
@@ -78,6 +78,6 @@ public class BrushModel
             mr.reflectionProbeUsage = ReflectionProbeUsage.Off;
         }
         
-        go.transform.SetPositionAndRotation(Vector3.zero, Quaternion.Euler(-90, 90, 0));
+        go.transform.SetPositionAndRotation(Vector3.zero, Quaternion.identity);
     }
 }

Assets/Scripts/Modules/RenderModule.cs

@@ -58,7 +58,7 @@ public partial class RenderModule
         aliasModels.Add(aliasModel);
 
         var go = new GameObject(modelName);
-        go.transform.SetPositionAndRotation(new Vector3(xPos, 0, zPos), Quaternion.Euler(-90, 90, 0));
+        go.transform.SetPositionAndRotation(new Vector3(xPos, 0, zPos), Quaternion.identity);
         
         aliasModel.Animate(0, out Mesh mesh, out float blendWeight);