The SuperKEKB is a high-luminosity electron–positron collider where the “nanobeam collision scheme” is utilized to achieve an unprecedented high luminosity. While its luminosity performance had gradually improved, it had been found that the SuperKEKB encountered some challenges as a luminosity frontier machine, such as severe beam instabilities—including sudden beam loss (SBL), low injection efficiency, and low machine stability. To overcome these challenges, we enforced a long shutdown (LS1) from July 2022 to January 2024 to perform numerous upgrades, including the construction of a nonlinear collimation (NLC) system and modification of the injection point. The first commissioning after the LS1 was conducted from January to July 2024. Even though the SBL was the major issue, several new findings emerged from the commissioning. Based on these, it was suggested that dust may cause the SBL. The injection efficiency was considerably improved during the last 2 weeks of the commissioning. To our knowledge, the effectiveness of the NLC for the strange beam background noise of the physics detector was demonstrated for the first time. The peak luminosity was 4.47x10^34 cm-2s-1 with a vertical beta function at the interaction point of 0.9 mm, and the integrated luminosity during this run was 103 fb-1.