The implantation of neural probes results in focal Traumatic Brain Injury (TBI), subsequently triggering a local neuroinflammatory response. Microglia, the brain's resident immune cells, exhibit distinctive transcriptional and morphological shifts upon activation, serving as a frontline defense against cerebral damage or infection. However, limited information exists regarding the spatial organization of these shifts during recovery. In this study, we tracked changes in the spatial organization of activated microglial phenotypes around the injury zone across a chronic period of 18 weeks after focal TBI (N=50). To enable a high-throughput morphological analysis, we developed an automated cell segmentation and analysis framework. Our pipeline allowed the detection of 79 distinct morphological parameters in a population of over 400,000 microglia. Morphological trajectory analysis elucidated a taxonomy of 14 diverse morpho-types, categorized into four major phenotypes: ameboid, highly ramified, transitional, and rod-like, each distinctly distributed across activated, intermediary, and homeostatic zones. Furthermore, trajectory analysis substantiated the alteration in morphology via nonlinear bidirectional activation pathways. Our analysis further revealed a prominent surge in microglia density during the acute phase(>2 weeks), indicating pronounced proliferation/migration towards the injury site. This surge in local Iba+ microglial cells was lost at later time points, with a return to but not complete homeostasis at 18 weeks post-injury. In summary, this study aimed to elucidate the spatio-temporal alterations in microglial populations by means of morphological changes across tissue recovery after focal TBI. The analysis framework can be openly accessed through: https://github.com/vatsal-jari/MicroFace.github.io