How to make a combat map with set points?

Hey everyone, I’m new to Godot, but have some coding experience. Please bear with me as a newcomer.

I’m creating a tactics RPG with a unique map system that isn’t the standard grid system. I simply need the ability to set specific locations on the map for the characters to move between.

With the picture as reference, each hexagon is a location for the characters to end their turn on. Each location has a path to each adjacent location (diagonals included), creating a spider web-like set of paths.

I was able to get this working to about 90% on unity, but instead of starting from scratch again, I’d prefer some pointers. I can figure out pathing and the like, but I haven’t got a clue for making the locations and paths themselves atm.

I’m also doing this in Godot 3D as I want to be able to add vertical positions as I progress, in case that changes things. Thanks in advance!