To understand the file, you have to understand the hardware. Every Nintendo 3DS console contains a dedicated security processor known as the . This processor handles the initial boot process, encryption, and security checks.
boot9.bin — 32 kilobytes of machine code — was injected directly into the boot ROM's shadow space. It wasn't permanent, but it was alive. The 3DS booted. The familiar popping sound of the home menu echoed through the silent basement.
boot9strap is installed into the FIRM0/1 partitions, into BootROM. boot9.bin is required only if you need to rebuild or verify boot9strap after a system failure.