To access the download:
• Launch Assassin's Creed: The Rebel Collection.
• Select Assassin's Creed Rogue from the main menu.
This should open the Nintendo eShop.
• Choose Download.
• Relaunch the game once the download finishes.
Selecting Assassin's Creed Rogue from the main menu will now launch the game.
Please note that downloading the digital version of the game from the Nintendo eShop will automatically download both games.