1) "What's true is determined by the scientific method" is, in fact, an axiom based on the old "obviously true" assumption.
2) There is thus far no evidence that the scientific method can deduce what the universe is and why it came into being. So according to the scientific method, we should probably be concluding that the truth isn't determined by the scientific method. It is a window into a fairly small subset of the truth.
3) We don't use the scientific method in court cases, we use standards of evidence and reasonableness tests. So when it matters what the truth is we don't use science (and, indeed, probably could not because it is too limited to achieve fairness).