Cell death shapes multicellular organism development and sustains tissue and organ homeostasis. Over the past decade we have begun to understand the breadth of physiological and biochemical diversity in cell death and clearance pathways, which play vital roles in organismal development and heath. While apoptosis and necrosis have been studied extensively across many model systems and contexts, the discovery of non-apoptotic paradigms of cell death and their roles in disease has greatly expanded the field. Collectively called Regulated Cell Death (RCD), these death pathways are regulated in a tissue and context-dependent manner (e.g. disease state). This dissertation is a culmination of multiple projects investigating cell death and clearance events spanning the ovary and the brain of the model organism, Drosophila melanogaster. We undertook the first multi-modal, high-throughput survey, involving single-cell RNA-seq, TRAP-seq, and proteomics, to compare two different archetypes of germline death in the fly egg chamber - apoptosis and phagoptosis. Our analysis identified several important candidates and pathways that are either unique to or shared between the germline death modalities and affecting oogenesis upon their disruption. We also observed that V-ATPases, proton pumps required for germline phagoptosis, are differentially localized throughout oogenesis, and we identified the specific subunits upregulated in phagoptosis. Furthermore, we identified a novel exon splicing event in the ‘a’ subunit isoform of V-ATPases that may facilitate its sub-cellular localization. Using a novel image analysis method involving image segmentation and spatial statistical inference, we determined that circulating immune cells agglomerate at specific niches within the abdomen, in response to egg chamber degeneration resulting from physiological stress of protein-deprivation. We then turned our focus to phagocytosis in the fly brain, which is essential for pruning synapses and for the removal of dying neurons and misfolded proteins. Disruptions to glial phagocytosis results in a range of age-dependent neurodegenerative phenotypes, primarily exemplified by vacuolization of brain tissue. Using a pre-trained deep-learning model to perform image segmentation and 3D reconstruction of vacuoles, we characterized the severity of neurodegeneration in brains lacking the phagocytic receptor Draper in glia and further demonstrated that this phenotype is attenuated by knockdown of the NF-κB transcription factor Relish in flies lacking glial Draper. Collectively, the methods and results described herein will have applications beyond the Drosophila model and the field of cell death, with important implications in understanding fertility and the underpinnings of cognitive disorders.