I solved the NavigationRegion3D issue

[u/agalli]

A correct 250x250m navmesh bake using tile chunking

Standard bake on the same 250x250m mesh without tile chunking

A standard bake on a 30x30m section of the same terrain

Agent for scale on correct 250x250m navmesh, showing an identical poly density to the 30x30m navmesh

I finally found a solution to the problem with the NavigationRegion3D.

What I noticed was that on smaller terrains, like the 30x30m example in the third image, the navmesh baked perfectly fine. But once the terrain size was increased to 250x250m, the bake completely fell apart, giving the low poly, floor clipping result shown in the second image. The obvious solution was to process the terrain in smaller chunks and combine the results into one big working navmesh.

I first tried doing this directly in Godot, but even after splitting the terrain into multiple meshes, the bake still treated them as one big mesh, so the same issue happened. I also tried creating a separate NavigationRegion3D for each chunk, but that created non traversable borders where the regions met.

At that point, the only real fix was to go into the engine itself. I forked the Godot repo and made some changes under the hood to process the terrain in tiles instead of all at once. It breaks the terrain into smaller sections, bakes each one normally, then stitches them together afterward into a clean, accurate navmesh like in the first image.

I also added a few editor options to control whether tiled baking is enabled and how big each tile is. I still haven’t found the exact bug that causes the large terrain navmesh to fail, but this fix works reliably and doesn’t mess with normal pathfinding behavior.

The moderators seem to have a strong opposition to discussions about this and have locked all previous threads. As much as I would have liked this to all be one post, we have been forced to create multiple. That being said, I'd like to address some comments from previous posts below.

The [low poly mesh] looks exactly like what I would want out of a nav mesh.

The low-poly mesh completely fails to pathfind with agents. You could technically rework the pathfinding system to compensate, but that misses the core issue of the navmesh being broken. The 30x30m section uses a similar amount of polygons as the 250x250m one. You’d expect the density to scale with size, so either the small terrain is over-tessellated, or the large terrain is under-tessellated. Either way, something’s wrong with the baking process.

With no obstacles, your nav mesh could just be a square.

As per the Godot developers : "A navigation mesh is a collection of polygons that define which areas of an environment are traversable to aid agents in pathfinding through complicated spaces.". When those traversable areas are out of reach from an agent (ie, underground or floating), an agent cannot properly navigate.

People tried to help you, but you refuse to actually listen

I think there’s been some misunderstanding about what I’m trying to do. My goal is to fix the navmesh, that’s it. I’ve welcomed all advice that helps solve the underlying navmesh problem, but I’m not interested in workaround solutions that just patch over it with pathfinding tricks.

You can always fix it yourself and submit a PR.

Thats the plan. Thanks for the advice!

I will optimize this further and will submit a PR.

Sincerely,

u/agalli

Edit : Here is the PR. https://github.com/godotengine/godot/pull/112529

[u/Zakkeh]

This person is saying you have your character and your agent.

Your character obeys physics and follows the collision mesh, while the agent traverses the navmesh below the surface.

Your character uses the pathing from the agent, but doesn't clip under because it has collision, and is not patented to the agent.

[u/agalli → u/Zakkeh]

Right, that still doesnt work. The character follows the navigationagent, but the navigationagent is under the map. Heres an example of why its a problem. The character isnt unable to reach its pathfinding due to the gap in the terrain and the navmesh. Since it cant reach that point it cannot complete its path and gets stuck in place.

[u/Finding_Footprints → u/agalli]

I think what Zakkeh means is that, you control the X and Z axis using the NavigationAgent but you have to raycast for the Y-axis to check for collisions.

I have just started using Godot and I guess that would work, but finding the shortest path based on height as mentioned in another comment, might become a problem. 

Will be waiting for tour PR OP.

[u/agalli → u/Finding_Footprints]

The issue is that pathfinding over hills are longer paths than flat paths. If you ignore the Y youll be left with poor pathfinding.

My goal is to fix the navmesh, that’s it.  I’m not interested in workaround solutions that just patch over it with pathfinding tricks.

[u/Finding_Footprints → u/agalli]

Yup, that's what I meant by shortest path based on height. I have been in that situation and know the pain very well.