I would like to cross the two over in the future. We've done a story based on the Hunters, and this time around we're doing a story on the Galactic Federation. In terms of story, Tanabe desired to further explore the background of Sylux, the anti- Galactic Federation Bounty Hunter from Metroid Prime Hunters, who he confirmed was the pilot of the mysterious spacecraft at the end of Corruption: 'Personally I'd like to create a story centring around Sylux and Samus. Tanabe suggested that a fourth game might be set on a single planet and feature a time-shifting mechanic. While nothing is known yet of the game's plot, Tanabe had revealed some of his ideas for a future Metroid Prime game in an interview regarding Metroid Prime: Federation Force in 2015. For instance, I think I can come up with some unique ideas using the Morph Ball, which is a specific skill of Samus.' Speaking to Kotaku in 2009 after the release of Metroid Prime Trilogy, Tanabe hinted at future Prime installments, and the potential to expand upon the multiplayer mode in Metroid Prime 2: Echoes: 'We will keep considering multiplayer for the Prime series. The game's original incarnation was described as 'return to the first-person adventure roots of the original Metroid Prime game and introduc a new storyline that ties together the events of the Metroid Prime universe and takes the storyline in new directions,' though it is unclear whether these plans have changed with the game's development being restructured.

In January of 2019, it was announced through the Nintendo Switch news system that the game's development was not living up to the standards of the series, and so development had been restarted from scratch with Retro Studios working under Tanabe instead. The game was originally developed by a 'talented new development team' led by Kensuke Tanabe, the longtime producer of the Prime series.

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