In this Letter, we study how cooperation is organized in complex topologies by analyzing the evolutionary (replicator) dynamics of the prisoner's dilemma, a two-player game with two available strategies, defection and cooperation, whose payoff matrix favors defection. We show that, asymptotically, the population is partitioned into three subsets: individuals that always cooperate (pure cooperators), always defect (pure defectors), and those that intermittently change their strategy. In fact, the size of the later set is the biggest for a wide range of the "stimulus to defect" parameter. While in homogeneous random graphs pure cooperators are grouped into several clusters, in heterogeneous scale-free (SF) networks they always form a single cluster containing the most connected individuals (hubs). Our results give further insights into why cooperation in SF networks is enhanced.