The scientific method will never yield the theory of everything. The scientific method is based on observation. That means that the nature of unobservable universe, which cannot be observed, is out of the reach of science. Just because something is true of the observable universe, does not mean that it must be true of the unobservable universe, or the entire universe. To say that it does, would be a fallacy. It's called the fallacy of composition. Take the expansion of the observable universe for example, if it is true of the observable universe it doesn't mean you can judge whether or not it's true of the unobservable universe using the scientific method. If it was not true of the unobservable universe, then it would not be a property inherent in the nature of gravity.
So, in order to have a theory of everything which shows the fundamental laws governing the nature of the entire universe, both observable and unobservable, science and the scientic method which it is based upon must be shelved as a non-satisfactory method to accomplish that goal.
The only way to discover a theory of everything for the whole universe is not through science and physics, but through something which is not reliant on observation: logical truth. That's why all the particle physicists and cosmologists who work to look for a fundamental theory of everything do so in vain, as they cannot say their observations are true of the unobservable universe since they can't observe it, and also they mightn't be even able to observe the universe at the smallest possible length if it is smaller than anything attainable by humans, or if there is no smallest possible lenght, and everything is always divisible, they wouldn't be able to do it in either case. And to assume that the smallest observed lenght is the smallest possible length in the universe is naive.