Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fate of individual organisms differently1-4. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve5-8. Here, we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an inter-compartmental signaling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable “twin” spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we could systematically tune the penetrance of each mutant fate. Furthermore, signaling and replication perturbations synergize to dramatically increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum showed a strong resemblance to twin sporulation in these B. subtilis mutants9,10. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.