It is clear that within the field of archaeological computational modeling, the detection and reduction of uncertainty have played far too marginal a role. To highlight why it is important to grapple with such uncertainty, this concept is here treated from a broader conceptual perspective. Perhaps most central to this endeavor is that researchers aiming to reconstruct any system, be it past or present, must confront the fact that uncertainty can never be avoided completely, as the world constitutes a place of nearly limitless possibilities. Moreover, in transforming the natural systems in which we live, we affect infinitely more dimensions of the system than we know, leading to numerous unanticipated consequences. This renders the task of analytically reconstructing the past nearly impossible. This paper discusses uncertainty in relation to traditional, reductionist science as well as with respect to complex systems science. Complex systems meet head on the issue of expanding possibilities, seeking to investigate the breadth and depth of these phenomena. In view of all this, it is argued that, rather than attempt the unattainable by reconstructing models of human reality, archaeological modelers would do well to utilize modeling as a “tool for thought” to enhance interpretations of past socio-natural processes and transform theoretical and methodological approaches.