Vanadium dioxide(VO$_2$) is a paradigmatic example of a strongly correlated system that undergoes a metal-insulator transition at a structural phase transition. To date, this transition has necessitated significant post-hoc adjustments to theory in order to be described properly. Here we report standard state-of-the-art first principles quantum Monte Carlo (QMC) calculations of the structural dependence of the properties of VO$_2$. Using this technique, we simulate the interactions between electrons explicitly, which allows for the metal-insulator transition to naturally emerge, importantly without ad-hoc adjustments. The QMC calculations show that the structural transition directly causes the metal-insulator transition and a change in the coupling of vanadium spins. This change in the spin coupling results in a prediction of a momentum-independent magnetic excitation in the insulating state. While two-body correlations are important to set the stage for this transition, they do not change significantly when VO$_2$ becomes an insulator. These results show that it is now possible to account for electron correlations in a quantitatively accurate way that is also specific to materials.