If we were, somehow, to have two identical systems (two identical universes), their future histories would be exactly the same. It would be impossible for them to be different.
What if the physical laws by which the systems evolve have built in randomness (a la quantum theory)? Then the two systems could diverge at every quantum level operation and interaction and follow very different paths. That sort of randomness would not constitute free will as generally conceived but it would mean the end states are different and only calculable as probabilities rather then the more clockwork model you envisage.