I can see how the saying, "correlation is not causation," might make you think that causation is not mathematical. Nothing could be further from the truth. Correlation is not causation, but statistics encompasses more than mere correlation.
Judea Pearl's approach to causation is a successful one, and I'd recommend checking out his book.
In statistics, we can build non-causal models, and we can build causal models. A typical Bayesian network, or a linear regression, is an example of a non-causal model. What Pearl calls a "causal Bayesian network" is an example of a causal model. An example of a causal model that is not probabilistic is Conway's game of life. What causal models have in common is that you begin with some initial conditions, and deduce immediate effects of those conditions, and then deduce effects of the effects, and so on. Deduction in a causal model doesn't usually go "backwards" - it can go backwards, but there is a preferred forward direction from causes to effects, which lines up with the temporal order of events, with causes happening prior to effects.
So to find a "causal story," you build a model of a process, where the model is - by design - causal. Then you check how well the model fits the observations. If the model fits well, then you have a causal story. You can try this for many different causal models to find the ones that fit the best without being too complicated (Occam's razor).
One way to distinguish causation from correlation is by looking at what kind of questions you can ask and answer. If you have a non-causal model, you can ask and answer questions of the form, "If X had been observed to take the value x, what would the distribution over Y be?" If you have a causal model, you can also ask and answer questions of the form, "if X had been set to the value x, what would the distribution over Y be?" Pearl's causal Bayesian networks allow for this second kind of query.