M17: Infestation has a goal of destroying a facility used to raise Metroids. The side objective is for a player to return a Metroid Egg with them. This side objective is notably canon as General Alex Miles' debriefing requests one be returned for research purposes.
Furthermore, upon beating the game after clearing this side objective, a bonus post-credits cutscene is shown in which Spoiler:Sylux, from Metroid Prime Hunters, breaks into a Galactic Federation facility, with a Metroid freshly hatched.

At E3 2015, Nintendo unveiled a new game as an event played during the Nintendo World Championships competition entitled "Blast Ball", with many in attendance noting the game's resemblance to Metroid Prime Hunters. Days later, during the 2015 Nintendo Digital Event, Blast Ball was announced to be part of a full-fledged Metroid Prime spin-off game entitled "Metroid Prime: Federation Force". The game received heavy critical and fan backlash upon its reveal, with common complaints including the choice to reveal a Metroid Prime spin-off title almost ten years after the last traditional Metroid Prime game and after a six-year gap from the similarly polarizing Metroid: Other M, the utilization of a chibi art style, and a seeming lack of Samus Aran or a single-player mode (Samus would later be revealed to be in the game as a side-character and single-player functionality was later confirmed during E3). The reveal trailer received a heavy dislike-to-like ratio on YouTube, having at least 87,000 dislikes and only 10,000 likes as of this writing. Furthermore, a Change.org petition to cancel the game received 7,500 signatures 24 hours after its creation, and received 24,108 signatures prior to its closure.

Nintendo acknowledged the negative pre-release reception of the game several times, but still defended the game overall, with Shigeru Miyamoto and Nintendo of America president Reggie Fils-Amie giving similar statements about trying to propel the Metroid series by challenging the traditional gameplay formats that came before it and made up the essence of the franchise. Fils-Amie also compared the fan reaction to the game's reveal to that of The Legend of Zelda: The Wind Waker, which also received heavy criticism for its art style and gameplay compared to The Legend of Zelda: Ocarina of Time and The Legend of Zelda: Majora's Mask. The game's co-producer and Metroid Prime series producer Kensuke Tanabe on the other hand had much more conflicting reactions, initially stating that he had expected the negative reception, but later remarking that he was quite surprised by the negative reception and criticized the heavy criticism against the game's graphics, but in both cases he still asked players to reserve their judgements until they played the game.

During the March 3, 2016 Nintendo Direct five months prior to the game's release, an entire segment of the Direct dedicated to the game was hosted by Tanabe, where he addressed fan criticism, explained the development history of the game, showed a more in-depth view of the story mode, and offered a glimpse of Samus' role in the game. Some people believed this segment of the Direct showed that Nintendo was doing "damage control" for the game after the criticism it received at its reveal. Fan reception did not improve, as shortly after the release of the Direct and a subsequent trailer, it started to receive thousands of dislikes like the reveal trailer, prompting Nintendo to disable the like/dislike ratio. Metroid Prime: Federation Force was noticeably absent during E3 2016, but would receive more coverage and trailers from Nintendo in the immediate weeks leading up to its release, where it ultimately received a mixed to average reception from critics and fans.