Adaptive laser pulse shaping has proven to be expeditious for discovering laser pulse shapes capable of manipulating complex systems. However, if adaptive control is to be a valuable interrogative technique that informs physical and chemical research, methods that make it possible to infer mechanistic information from experimental results must be developed. Here, we demonstrate multivariate statistical analysis to extract a single control variable from results of a 137-parameter adaptive laser pulse-shaping optimization of multiphoton electronic excitation in a ruthenium(II) coordination complex in solution. We show that this single variable can be used to linearly manipulate the observed fitness, which is determined by the ratio of molecular emission to second harmonic generation of the laser pulse, over the range explored during the adaptive optimization. Further, manipulation of this variable reveals the latent control mechanism. For this system, that mechanism entails focusing the second harmonic power spectrum of the laser field in a spectral region where the probability of two-photon absorption by the molecule is also large. The statistical tools developed are general and will help elucidate control mechanisms in future adaptive pulse-shaping experiments.