Windows Authentication - require additional password for special users

I think I would try to use MVC Filters : https://docs.microsoft.com/en-us/aspnet/core/mvc/controllers/filters?view=aspnetcore-2.2#authorization-filters

Filters run after all Middleware, but before the Action. This will allow you to control the redirect to credentials page just for specific actions or controllers. Whilst normally this is not the recommended method for authorization, I think it fits your requirements for a hybrid secondary authentication.

public class SuperUserFilter : Attribute, IAuthorizationFilter
{
    public void OnAuthorization(AuthorizationFilterContext context)
    {
        if (context.HttpContext.Request.Cookies.TryGetValue("SuperUserCookie", out string cookieVal))
        {
            if (!IsValidCookie(cookieVal))
                context.Result = LoginPage(context);

        }
        else
        {
            context.Result = LoginPage(context);
        }
    }

    private bool IsValidCookie(string cookieVal)
    {
        //validate cookie value somehow
        // crytpographic hash, store value in session, whatever
        return true;
    }

    private ActionResult LoginPage(AuthorizationFilterContext context)
    {
        return new RedirectToActionResult("SuperUser", "Login",
            new {redirectUrl = context.HttpContext.Request.GetEncodedUrl()});
    }
}

Then you create a Login Controller

public class LoginController : Controller
{    
    [HttpGet]    
    public IActionResult SuperUser(string redirectUrl)
    {
        // return a page to enter credentials
        // Include redirectUrl as field
    }

    [HttpPost]
    public IActionResult SuperUser(LoginData loginData)
    {
        // Validate User & Password
        Response.Cookies.Append("SuperUserCookie", "SomeValue");
        return Redirect(loginData.RedirectUrl);
    }
}

Then you can decorate specific actions (or controllers) as required:

public class MyController : Controller
{
    [HttpGet]
    [SuperUserFilter]
    public IActionResult MySensitiveAction()
    {
        // Do something sensitive
    }
}