Plants respond to biotic and abiotic factors in the external environment. These include wounding, pathogen and pest attack, and changes in light and temperature. They also respond to internal signals produced during development, such as during the formation of flowers. These responses generally involve the re-programming of gene expression. Biotic and abiotic stress signal perception responses have commonly been represented as three pathways, which can be distinguished by the production of jasmonates, ethylene or salicylic acid. Each of these pathways therefore involves the perception of the stress, the synthesis of the signal molecule, the perception of the signal molecule and the ensuing response. An added complication is that these signalling pathways act both locally, at the point of the stress, and systemically. Much of what we know about these signalling pathways has come from studies of responses to the signal molecules, and of mutants altered in the production of, or sensitivity to, these signal molecules. This has provided clear indications that the pathways interact significantly. Because biotic and abiotic stresses induce the production of all three of these signal molecules, albeit in differing amounts, it is more appropriate to view the response output as the integration of a signalling network that involves the production of jasmonates, salicylic acid and ethylene. In this review, we provide an update on the regulation of jasmonic acid biosynthesis and the suggested roles for different biologically active intermediates in this pathway in Arabidopsis, and describe the jasmonate signalling mutants identified so far. We also examine how outputs from the jasmonate, salicylic acid and ethylene signalling pathways are integrated in the regulation of stress response and plant development. We use Boolean gates as a tool to represent the molecular networks and provide a qualitative description of the transmission of the signals. Finally, we illustrate how protein degradation, a common mechanism regulating many plant processes, may act as the ultimate level of integration between signalling pathways.