You will need Calibre for the command-line tools. You cannot simply take the exec files out of the app as there is a dependancy issue. No matter. Store Calibre somewhere - perhaps on the external drive if you so wish.
To convert a single ebook one would navigate to the Calibre app, explore the package and find ebook-convert in the MacOs folder. Drag this into the terminal followed by the ebook. Specify the output including the file extension which will determine the format. Done.
To convert multiple ebooks at once you will find it’s a tad bit more involved but really quite simple. Use the following code-snippet as a guide:
for book in \*.epub; do echo "Converting $book"; ebook-convert "$book" "$(basename "$book" .epub).mobi"; done
Navigate to the folder containing the ebooks. In place of ‘ebook-convert’ drag in the file from the Calibre app and change the file extensions to whatever makes sense. The program will proceed to convert all books specified.