First, the function Empty() {} representation is V8 stuff.
In V8, the Function.prototype object has "Empty" as the value of the Function.prototype.name property, so I guess you are probably using the Chrome's Developer Console, and it displays the name of the function in this way.
The name property of function objects is non-standard (not part of ECMA-262), that's why we see differences between implementations.
Now, Function.prototype is a function, that returns always undefined and can accept any number of arguments, but why?. Maybe just for consistency, every built-in constructor's prototype is like that, Number.prototype is a Number object, Array.prototype is an Array object, RegExp.prototype is a RegExp object, and so on...
The only difference (for example, between any function object and Function.prototype) is that obviously Function.prototype inherits from Object.prototype.
it seems everything in javascript start from Object.prototype, am I right about that?
Well, you're right Object.prototype is the last object of the prototype chain of most objects, but in ECMAScript 5, you can even create objects that doesn't inherit from anything (just like Object.prototype is), and form another inheritance chain, e.g.:
var parent = Object.create(null),
child = Object.create(parent);
Object.prototype.isPrototypeOf(parent); // false
Object.getPrototypeOf(parent); // null
Object.getPrototypeOf(Object.prototype); // null