Metroid Prime 3 marked the conclusion of the Metroid Prime trilogy, as well as Kenji Yamamoto's last foray into the Metroid universe (at least so far), this time assisted by Minako Hamano and Prime veteran Masaru Tajima. While the infusion of orchestral elements is something entirely new to Metroid, the soundtrack also contains a range of atmosphere unseen in previous titles, from the somber, tribal chanting of "Bryyo" to the aerie melancholy of the forgotten Chozo paradise of "SkyTown". However, there is also a strong undercurrent of sadness permeating the soundtrack, as emphasized by the sweeping percussion and choir of the "Title Theme". Indeed, this melancholy is also expressed though boss themes such as the epic "VS. Rundas" and mystical "VS. Gandrayda", the themes of two heroes possessed and destroyed by an evil beyond their comprehension. Perhaps this is not just simply channeling the narrative and themes of lost civilizations and friends destroyed by corruption, but also a realization that this is the final encore for the Prime series.

Corruption does contain its fair share of "atmospheric minimalism", but it executes this with a somber and eerie touch that goes beyond the 2001-esque howls of the Echoes soundtrack. For instance, "Xenoresearch" takes measured, cautious strides through the Metroid research lab, "Bryyo Fire" oozes with primal vulcanism, and "The Corruption" is a disturbing, cinematic piece that occurs only in the cutscene where Samus learns she is being corrupted by Phazon. This tension and dissonance is a defining factor of the Metroid series, states Yamamoto in an interview, and is counterbalanced by the joyful harmony seen through the "Ending Staff Roll" (here with the voiceover edited out).

Yamamoto also made nostalgia a key component of the soundtrack through the remixing of old favorites. "Theme of Super Metroid" makes a triumphant retun in the form of "Galactic Federation Theme", which is an immediate pleaser to old fans of the series. The reemergence of "Crateria - The Space Pirates Appear" in the form of "Pirate Homeworld" also sent smiles to longtime fans, while "Bryyo Ice" appeals to Prime veterans. Finally, "VS. Meta Ridley" was also given a Phazon metal overhaul through "VS. Omega Ridley".

The original, shorter US version of "Bryyo" is found in the extras section below (it was replaced with the Japanese version in the Trilogy re-release). Included as well is the Metroid Prime Trilogy "Title Theme", a fantastic finale to the Prime saga.