Plants grow and reproduce within a highly dynamic environment that can see abrupt changes in conditions, such as light intensity, temperature, humidity, or interactions with biotic agents. Recent studies revealed that plants can respond within seconds to some of these conditions, engaging many different metabolic and molecular networks, as well as rapidly altering their stomatal aperture. Some of these rapid responses were further shown to propagate throughout the entire plant via waves of reactive oxygen species (ROS) and Ca2+ that are possibly mediated through the plant vascular system. Here, we propose that the integration of these signals is mediated through pulses of gene expression that are coordinated throughout the plant in a systemic manner by the ROS/Ca+2 waves. Recent studies reveal that plants respond within the seconds to minutes time-scale to different biotic and/or abiotic stimuli. The rapid response of plants to different stimuli spans many metabolic, molecular, and biochemical pathways, and involves genes essential for plant acclimation or defense. Stomata can respond within minutes to different stimuli, such as ozone, pathogen infection, or light stress, and this response can be propagated from the affected leaf to different systemic leaves by the ROS/Ca2+ wave. Different transcriptional regulators display a triphasic expression pattern with transient peaks of expression at the seconds, minutes and hours time-scale. These regulators may shape the acclimation and/or defense response of plants in pulses of gene expression that orchestrate the gene response network. Rapid responses and the rapid systemic signaling pathways they activate could coordinate the systemic response of plants to a combination of different environmental conditions, enhancing the overall acclimation and ability of plants to withstand the rapidly changing conditions within their environment.