Certain commercial video games, such as Portal 2 and Tetris, have been empirically shown to train spatial reasoning skills, a subset of cognitive skills essential for success in STEM disciplines. However, no research to date has attempted to understand which specific features in these games tap into players' spatial ability or how individual player differences interact with these game features. This knowledge is crucially important as a first step towards understanding what makes these games effective and why, especially for subpopulations with lower spatial ability such as women and girls. We present the first empirical study analyzing the relationship between spatial ability, specific game features, and individual player differences using a custom-built computer game. Twenty children took a pretest of spatial skills and then played our game for 2 hours. We found that spatial ability pretest scores predicted several player behaviors related to in-game tasks involving 3D object construction and first person navigation. However, when analyzed by gender, girls' pretest scores were much less predictive of player behavior.