You need to download it from the guide, probably with a torrent client like deluge or bittorrent
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"Note that the following required file named secret_sector.bin is the same one that was found in the various data_input.zip file versions. If you already have that file on your disk somewhere, you can use that one instead of downloading the one below.
Note that, only on New 3DS, secret_sector.bin is needed to revert the arm9loaderhax exploit, which is why it is not needed for the installation of boot9strap on a stock console. If you do not have a New 3DS, you do not need secret_sector.bin."