Our objective was to apply ideas from complexity theory to derive expanded neurodynamic models of Submarine Piloting and Navigation showing how teams cognitively organize around task changes. The cognitive metric highlighted was an electroencephalography-derived measure of engagement (termed neurophysiologic synchronies of engagement) that was modeled into collective team variables showing the engagement of each of six team members as well as that of the team as a whole. We modeled the cognitive organization of teams using the information content of the neurophysiologic data streams derived from calculations of their Shannon entropy. We show that the periods of team cognitive reorganization (a) occurred as a natural product of teamwork particularly around periods of stress, (b) appeared structured around episodes of communication, (c) occurred following deliberate external perturbation to team function, and (d) were less frequent in experienced navigation teams. These periods of reorganization were lengthy, lasting up to 10 minutes. As the overall entropy levels of the neurophysiologic data stream are significantly higher for expert teams, this measure may be a useful candidate for modeling teamwork and its development over prolonged periods of training.