Oceanic plankton are sensitive to physical and biochemical changes in the surface ocean, and are key modulators of the ocean carbon cycle via photosynthesis and calcification. Fossil plankton remains exported to the seafloor and preserved in sediments thus hold key clues on both past climate changes as well as associated biological responses and feedbacks. The western equatorial Indian Ocean (WEIO) is a major player in tropical ocean-atmosphere climate dynamics, with far-reaching impacts on global climate patterns. In 2021, the SCRATCH cruise onboard the research vessel Marion Dufresne II collected high-quality, complete sediment cores spanning the Pleistocene (last ~2 million years) from the WEIO, with the aim of resolving past climate variability and volcanic activity in this important region. Here, we propose to study the co-evolution of plankton, coral reefs, and climate over the Pleistocene. We will perform paired paleogenetic, biomarker, and microfossil analyses, as well as reconstruct key paleoceanographic variables to constrain background climate change, in four sediment cores recovered during SCRATCH. Using state-of-the-art methodologies across three partner institutes, we will combine expertise on paleoceanography, organic geochemistry, genetics, and micropaleontology to address the hypothesis that cyclical changes in the morphology of plankton fossils represent genetic evolution, forced by external climate cycles. Anticipated results will (1) provide a comprehensive picture of paleoceanographic evolution of the WEIO, including Indian Ocean Dipole mean state, (2) demonstrate for the first time the relationship between genetic and morphological plankton evolution in multiple groups, and (3) shed light on external (climatic, volcanic) drivers of evolution, plankton community dynamics, and pelagic versus neritic marine productivity.