It ends the turn, bringing up a menu, effectively a "pause". Unfortunately, at that point, you have to dig through the menu, to unselect the option to disable the auto-turn-end.
No other menu will interrupt the process. The game will continue to run, behind the screens, including the in-game selection menus, where it honestly should be pausing the game.
I agree, this needs a readily available, simple, toggle on the UI screen. A simple three-stage RED/YELLOW/GREEN cycle, unless you only want RED/GREEN for on and off. Yellow being some custom tween phase, with a nice little delayed time-pause, at the end, where you can jump right to STOP, next. (Yes, on a fast computer, and in some actions, things fly by too fast to even figure-out what is happening at all.)
Honestly, having the option, with a little pop-up screen, would be nice. Let you pick the things you want to "skip", or things you want a "full-stop" on, for automation. (Having smart AI auto-explore would be nice. As opposed to having it be a full-stop, every time. Duh... Get the huts and avoid bandits and enemies!)
The one feature, which still has higher demand than any of the crap they added in every version, yet, they still have not added this simple feature. (This is one of those "play it my way", games. "They", being the developers, who rarely actually play the game, beyond testing. Or, they only care about how they want to play it. It's a total hacked oversight. Which is why they still don't have it working right, when it is on. Thus, everyone just surrenders and turns it off, eventually, forever.)
Actually, what we need is an "Auto-play, while key is pressed". Something like the "Space-bar", so we can just hold it, or rest something heavy on it. While it is being held down, it runs blind, in auto-end-turn. Let go, and it stops on the next possible turn, which is yours. Pure, "Keep it simple stupid", solution, by "Keeping it stupid simple".
Maybe on Civ MCXVII, we will get this feature.