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The Nintendo eShop is the digital online store for the Nintendo 3DS, Wii U and Nintendo Switch consoles. It replaces the Wii Shop Channel of the Wii. From the eShop, players can buy games, videos and demos. Some classic Nintendo games have been re-released on the eShop via Virtual Console. The eShop on all three consoles became available on their respective launch dates.

Metroid Prime Trilogy advertisement.

All Metroid games with the exception of Metroid Prime Pinball are available through either or both eShops in some form. Through the 3DS Ambassador Program, players were able to earn the original Metroid and Metroid Fusion for free via the eShop. While Metroid was released onto the public eShop on March 1, 2012, Fusion remains exclusive to Ambassadors and has yet to be re-released publicly. It is available on the Wii U eShop, along with Metroid: Zero Mission, Metroid Prime Hunters and Metroid: Other M. Metroid II: Return of Samus was released in November 2011 on the 3DS eShop, its first port since the original release.

Super Metroid was made available on the Wii U's eShop from May 15, 2013 to June 13, 2013 as part of the Wii U Virtual Console Trial Campaign. This version allows for GamePad-only play and customizable controls. Those who ownedSuper Metroid on the Wii Virtual Console were be able to get it on Wii U for a reduced price. On April 14, 2016, the game was be re-released once again through an improved Virtual Console, exclusively on the New Nintendo 3DS XL.

Metroid Prime Trilogy was released on the Wii U eShop on January 29th, 2015 at half price for a week, before reverting to full price. Metroid Prime: Blast Ball, a demo for Metroid Prime: Federation Force was released on the 3DS eShop unannounced on July 21, 2016.

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