Starting with (released in late 2021), the developer SciresM consolidated the boot process. The two-file system was replaced by a single unified payload called simply fusee.bin , and the secondary stage data was moved into a package file located at /atmosphere/package3 . Because of this change:

The boot process of a Nintendo Switch involves several stages, starting from the bootrom (fusee) through the bootloader, and then to the system firmware. fusee-secondary.bin comes into play after an exploit has been successfully executed in an early stage of the boot process. It is designed to:

infiniteichiwon commented. ... @SciresM I got a fatal error saying: Failed to stat stage2 (atmosphere/fusee-secondary. bin)! what ... GitHub switch-guide/docs/extras/updating.md at master - GitHub Still running into issues? ... If you update from below Atmosphère 1.0. 0, there are additional steps to follow. You will have to ... GitHub

In summary, fusee-secondary.bin is the main payload file used to boot into custom firmware on a hacked Nintendo Switch.

The primary purpose of fusee-secondary.bin is to be loaded after the initial exploitation phase, providing a bridge to further compromise the system or to load custom firmware (CFW) on the Nintendo Switch. It acts as an intermediary step that helps in overcoming the limitations of the initial exploit, allowing for more comprehensive access to the system's functionalities.