Abstract The Asian sector is reported to have experienced a strong electron density enhancement during the May 2024 super geomagnetic storm between local evening and sunrise. We present a high‐resolution 3‐D ionospheric reconstructions over Japan using computerized ionospheric tomography (CIT) facilitated by a dense Global Navigation Satellite System (GNSS) network. Results reveals storm‐enhanced density (SED) features characterized by increases in total electron content (TEC) and F2‐layer peak density (NmF2), elevated height (hmF2), and increased electron densities at higher altitudes. Spatially, the SED structures extended ∼ ${\sim} $1,000 km latitudinally and 300 km vertically. Within these enhancements, large‐scale electron density depletions, spanning over 600 km and aligned with geomagnetic field lines, were identified. We hypothesize these depletions as equatorial plasma bubbles (EPBs) that extend into mid‐latitudes while remaining embedded in the SED. These results, highlight the capability of GNSS‐based 3‐D CIT in extending a quantitative understanding of complex ionospheric features during extreme events.

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