Background:
Seismology has accumulated extensive observational data, yet modern statistical methodologies have rarely been applied comprehensively to seismic datasets. Consequently, several long-standing interpretations, including magnitude distributions and aftershock decay laws, may reflect analytical constraints rather than physical processes. Re-examining earthquake behaviour using contemporary statistical tools provides an opportunity to reassess empirical relationships and clarify persistent ambiguities in seismic patterns.

Objectives:
This study applies modern statistical methods to complete seismic datasets to reassess magnitude distributions, aftershock decay, and three-dimensional active-zone structure, testing whether systematic temporal variations, including precursory changes before major earthquakes, can be objectively identified.

Methods:
Earthquake data were obtained from the Japan Meteorological Agency and analysed without any filtering, using a 1° latitude–longitude grid. The grid with the highest count in each year was examined, except for 2011, which focused on the Tohoku earthquake hypocentre. All calculations were performed in R, with three-dimensional visualizations generated using the rgl package. Hypocentre distributions were projected onto plate boundaries using principal component analysis (PCA) in two stages: 3D-to-2D dimensionality reduction and boundary-specific projection. Maps were verified and appropriately transformed to align with square-based latitude–longitude diagrams for quantitative analysis.

Results:
Analysis of hypocentre distributions in Japan identifies two major subducting boundaries, the East and Southwest, connected by the shallow Seto structure. Three-dimensional visualisations and Principal Component Analysis reveal these boundaries as planar yet gently curved, with deeper earthquakes concentrated along the Sanriku plate. The Pacific Plate subducts beneath surrounding plates, influencing lateral displacement of the Philippine Sea Plate and creating complex stress patterns. Hypocentre counts increase prior to major events, while deeper earthquakes tend to exhibit higher magnitudes. Aftershock decay follows a half-life process, with energy release distributed heterogeneously across regions, indicating that seismic activity is controlled by interactions between plate geometry, depth, and elastic properties. These findings provide a more robust framework for interpreting seismicity, revising plate boundary models, and informing risk assessment in Japan.

Conclusion:
Modern statistical analyses clarified Japan's plate boundaries, revised Pacific and Philippine Sea Plate configurations, and updated aftershock decay models, revealing temporal magnitude decay. These findings enhance understanding of earthquake mechanisms, improve seismic hazard assessment, and highlight the need for continued monitoring to address potential false negatives.