(Not op, just an example)

I don’t know an optimal answer here. I see various discussions online about flight control variants. However, here is a simple example I set up out of curiosity. Maybe useful? I’d like to hear about what you end up with.

Project code at: https://github.com/pipehat/godot41_flight_controller_example

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plane controller script:

extends CharacterBody3D

var print_delay = 1
var next_print = 0
const SPEED_MPS = 500

func _physics_process(delta):
	var input_dir = Input.get_vector("ui_left", "ui_right", "ui_up", "ui_down")
	
	if next_print <= 0:
		print(input_dir)
		print("-z: ", -transform.basis.z)
		next_print = print_delay
	else:
		next_print -= delta
	
	var roll = -input_dir[0]
	var pitch = input_dir[1]
	
	rotate(transform.basis.z, roll * delta)
	rotate(transform.basis.x, pitch  * delta)

	velocity = -transform.basis.z * SPEED_MPS * delta
	move_and_slide()

Hard to tell without seeing your code and node tree, but I reckon you are probably rotating a child (specifically the mesh instance). You should be rotating the root spatial of your player scene.

Here's a nice tutorial vid - simpler arcade-like control than my example. Looks like this is for Godot 3.x but the concepts should translate to v4 pretty closely.

https://www.youtube.com/watch?v=RsrwmAme_WA