var numberOne= Number(window.prompt("Type a number", ""));
//in prompt I entered "99" and I get output NaN
var numberTwo = "99";
The reason this is happening is because window.prompt already returns a string. So when you enter "99", you are effectively trying to cast
'"99"' to a Number, which can't be done.
Please note that result is a string. That means you should sometimes cast the value given by the user. For example, if his answer should be a Number, you should cast the value to Number.