How do visual signals evolve from early to late stages in sensory processing? We explored this question by examining two neural correlates of spatial attention. The capture of attention and inhibition of return refer to the initial advantage and subsequent disadvantage to respond to a visual target that follows an irrelevant visual cue at the same location. In the intermediate layers of the superior colliculus (a region that receives input from late stages in visual processing), both behavioral effects link to changes in the neural representation of the target: strong target-related activity correlates with the capture of attention and weak target-related activity correlates with inhibition of return. Contrasting these correlates with those obtained in the superficial layers (a functionally distinct region that receives input from early stages in visual processing), we show that the target-related activity of neurons in the intermediate layers was the best predictor of orienting behavior, although dramatic changes in the target-related response were observed in both subregions. We describe the important consequences of these findings for understanding the neural basis of the capture of attention and inhibition of return and interpreting changes in neural activity more generally.