I'm relatively new to Godot, but my guess would be something like a "Game-Manager"-Node/Scene. It could keep track of the current map/level, the spawned enemies, the current wave, the next waves to come and win or lose conditions.
At least these are my two cents. As I said I just started using Godot (have played around with it and followed a couple of tutorials), but I already got some experience using Unity3D.
So if there is a better approach, I'd be very glad to know about it aswell.