UIWindow not showing over content in iOS 13

You just need to store strong reference of UIWindow that you want to present. It seems that under the hood view controller that presented does not references to the window.

Based on all the proposed solutions, I can offer my own version of the code:

private var window: UIWindow!

extension UIAlertController {
    func present(animated: Bool, completion: (() -> Void)?) {
        window = UIWindow(frame: UIScreen.main.bounds)
        window.rootViewController = UIViewController()
        window.windowLevel = .alert + 1
        window.makeKeyAndVisible()
        window.rootViewController?.present(self, animated: animated, completion: completion)
    }

    open override func viewDidDisappear(_ animated: Bool) {
        super.viewDidDisappear(animated)
        window = nil
    }
}

How to use:

// Show message (from any place)
let alert = UIAlertController(title: "Title", message: "Message", preferredStyle: .alert)
alert.addAction(UIAlertAction(title: "Button", style: .cancel))
alert.present(animated: true, completion: nil)

Here are the steps to present a view controller in a new window on iOS 13:

1. Detect focused UIWindowScene.

extension UIWindowScene {
    static var focused: UIWindowScene? {
        return UIApplication.shared.connectedScenes
            .first { $0.activationState == .foregroundActive && $0 is UIWindowScene } as? UIWindowScene
    }
}

2. Create UIWindow for the focused scene.

if let window = UIWindowScene.focused.map(UIWindow.init(windowScene:)) {
  // ...
}

3. Present UIViewController in that window.

let myViewController = UIViewController()

if let window = UIWindowScene.focused.map(UIWindow.init(windowScene:)) {
    window.rootViewController = myViewController
    window.makeKeyAndVisible()
}

I was experiencing the same problems while upgrading my code for iOS 13 scenes pattern. With parts of your second code snippet I managed to fix everything so my windows are appearing again. I was doing the same as you except for the last line. Try removing viewController.present(...). Here's my code:

let windowScene = UIApplication.shared
                .connectedScenes
                .filter { $0.activationState == .foregroundActive }
                .first
if let windowScene = windowScene as? UIWindowScene {
    popupWindow = UIWindow(windowScene: windowScene)
}

Then I present it like you do:

popupWindow?.frame = UIScreen.main.bounds
popupWindow?.backgroundColor = .clear
popupWindow?.windowLevel = UIWindow.Level.statusBar + 1
popupWindow?.rootViewController = self as? UIViewController
popupWindow?.makeKeyAndVisible()

Anyway, I personally think that the problem is in viewController.present(...), because you show a window with that controller and immediately present some 'self', so it depends on what 'self' really is.

Also worth mentioning that I store a reference to the window you're moving from inside my controller. If this is still useless for you I can only show my small repo that uses this code. Have a look inside AnyPopupController.swift and Popup.swift files.

Hope that helps, @SirOz