Anthropogenic methane (CH4) point sources drive near-term climate forcing, safety hazards, and system inefficiencies. Space-based imaging spectroscopy is emerging as a tool for identifying emissions globally, but existing approaches largely rely on manual plume identification. Here we present the Methane Analysis and Plume Localization with EMIT (MAPL-EMIT) model, an end-to-end vision transformer framework that leverages the complete radiance spectrum from the Earth Surface Mineral Dust Source Investigation (EMIT) instrument to jointly retrieve methane enhancements across all pixels within a scene. This approach brings together spectral and spatial context to significantly lower detection limits. MAPL-EMIT simultaneously supports enhancement quantification, plume delineation, and source localization, even for multiple overlapping plumes. The model was trained on 3.6 million physics-based synthetic plumes injected into global EMIT radiance data. Synthetic evaluation confirms the model's ability to identify plumes with high recall and precision and to capture weaker plumes relative to existing matched-filter approaches. On real-world benchmarks, MAPL-EMIT captures 79% of known hand-annotated NASA L2B plume complexes across a test set of 1084 EMIT granules, while capturing twice as many plausible plumes than identified by human analysts. Further validation against coincident airborne data, top-emitting landfills, and controlled release experiments confirms the model's ability to identify previously uncaptured sources. By incorporating model-generated metrics such as spectral fit scores and estimated noise levels, the framework can further limit false-positive rates. Overall, MAPL-EMIT enables high-throughput implementation on the full EMIT catalog, shifting methane monitoring from labor-intensive workflows to a rapid, scalable paradigm for global plume mapping at the facility scale.