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After following endless guides and running the bcdedit /set {bootmgr} path \EFI\ubuntu\grubx64.efi command from windows, dual boot works!

Alas, it only works while the USB is plugged in, otherwise we get the Grub2 bash.

How can I finish the job so that the Grub2 bootloader is installed on the Win8 side of things? Is that how I want to finish the job?

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It seems you have your BIOS/EFI configured to boot from USB HDD first and you have properly configured bootloader on USB HDD.

Now, as you want to install GRUB on the fixed HDD along with Windows, you need

  • GRUB config files on your fixed HDD and directly acessible to GRUB
  • GRUB installed to MBR of your fixed HDD

See grub-install for options to put config files in non-standard directory and make sure you point it to MBR of your fixed HDD. Moreover, I doubt if you can put GRUB config files on NTFS partition, so you may need to create at least small linux partition for booting. (I did not checked it)

Besides - I hope you already have a backup of your MBR?

Although, it looks like you do not need dual-boot menu when there is no external HDD. In this case my recommendation would be to restore MBR on Windows HDD so that it boots Windows when there is no external HDD attached, keep the bootloader on USB HDD configured for dual boot and keep the BIOS/EFI boot priority set to boot USB before fixed HDD. This does not require repartitioning of your HDD, and cleans the setup. The dual boot menu would be presented only when external HDD is attached.

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