Nintendo gave the development of Metroid Prime to the U.S. based Retro Studios in part due to the fact that the Metroid series, while being incredibly popular in the United States, has never sold as well in Japan.
This game, as well as the rest of the Prime series, takes place between the original Metoroido (1986) (or its remake Metroid: Zero Mission (2004)) and Metoroido II Return of Samus (1991) (or its remake Metroid: Samus Returns (2017)). Although series creator Yoshio Sakamoto initially called the Prime series 'gaiden' (sidestory) games, they are considered to be a "contained subsaga" and a canon (official) part of the Metroid timeline.
Kraid, the over-sized green adversary from Metoroido (1986) and Super Metroid (1994), was supposed to make an appearance in this game in the Phazon Mines (just like Ridley did), but he was left out because of time constraints. It was widely believed that he was replaced by the Omega Pirate, however it has been confirmed that both were originally meant to appear in the game.
Some music from earlier Metroid games was remixed for this game. For instance, the Tallon Overworld theme is a remix from the Brinstar theme from Metoroido (1986); the Magmoor Caverns theme is the same music that was played in Ridley's lair in Super Metroid (1994); and the Meta Ridley boss fight is a remix from the Ridley boss fight in Super Metroid (1994).
The game was originally going to have narration by Samus, but it was cut out of the U.S. version (it can still be found in the game's code). In the European version, it was replaced by opening and closing narration by an unknown male character. Text-only narration by Samus would feature for the first time in Metroid: Fusion (2002), and the first full Samus voice-over could be heard in Metroid: Other M (2010).