Loners, individuals out-of-sync with a coordinated majority, occur frequently in nature. Are loners incidental byproducts of large-scale synchronization attempts or are they part of a mosaic of life-history strategies? Here, we provide the first empirical evidence of naturally occurring heritable variation in loner behavior, using the social amoeba Dictyostelium discoideum. Moreover, we show that Dictyostelium loners, cells that do not join the multicellular life-stage, result from a dynamic population-partitioning process. Underlying this partitioning, we find evidence that each cell makes a stochastic, signal-based decision resulting in an imperfectly synchronized multicellular development affected by both abiotic (environmental porosity) and biotic (strain-specific signaling) factors. Finally, we predict that when strains differing in their partitioning behavior co-occur, cross-signaling impacts slime-mold diversity across spatio-temporal scales. Loners are therefore critical to understanding collective and social behaviors, multicellular development, and ecological dynamics in D. discoideum. More broadly, across taxa, imperfect synchronization might be adaptive by enabling diversification of life-history strategies.