The enzyme responsible for incorporating atmospheric CO₂ in the reactions of photosynthesis is called Rubisco, an ancient, large, multi-subunit enzyme with a major apparent weakness. In addition to incorporating CO₂, Rubisco can also bind O₂ and perform an oxygenation reaction with the substrate ribulose bis-phosphate. The results of this oxygenation reaction are one molecule of phopshoglycerate and one molecule of a 2-carbon product called phosphoglycolate. While the PGA can enter the reduction pathway in the chloroplast, the phosphoglycolate cannot and instead enters a recovery pathway spread across two other organelles, the peroxisome and mitochondria. The oxygenation reaction together with the various recovery steps are known as the photorespiratory pathway and represent a significant energetic cost to the plant.

There are probably many explanations for the existence of this costly pathway, beginning with a consideration of the conditions under which Rubisco evolved. Photosynthetic carbon reduction probably began over 1 billion years ago, and is itself thought to have been responsible for the formation of most of the O₂ in the atmosphere. In other words, in the earliest cases, there was little to no competition between CO₂ and O₂ for the active site of Rubisco. So the simplest explanation for why oxygenation happens is that there was not a selective pressure to discriminate between these two substrates. Another explanation is that, given the integration of the recovery pathway with various metabolic pathways such as amino acid biosynthesis, it represents a source of inputs to these pathways. A third explanation is that photorespiration is a strategy for the plant to cope with excess light energy under conditions in which CO₂ is limiting. Such conditions arise when the plant is water-stressed and closes stomata to conserve water, which results in a build-up of O₂ and draw-down of CO₂. Evidence for photorespiration as an important energy-shunting pathway comes from experiments in which mutants for various steps in the recovery pathway were isolated and grown under various conditions. Mutants grow normally under low-light conditions, but when challenged with light levels similar to full sun the mutants show symptoms consistent with damage due to photoinhibition.