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Silence made its debut in the first Metroid game. The high-pitched melody pierces through a repeating sequence of low-pitched notes. This is also included on Game Sound Museum ~ Famicom Edition ~ 12 Metroid. It can be heard here: 
Silence returns in Super Metroid. In this version, the low notes have been reinterpreted as an ambient drone. The melody is played with beeping tones, reminiscent of Morse code. An additional harmonic sequence of repeating beeps has also been added. It can be heard here:  An alternate version that strips away all the beeping, leaving just the ambient drone, plays during the Game Over screen and just before the second battle against Ridley:  Another remix is briefly heard during the end credits, heard here: 
Debuting in Super Smash Bros. Melee, Brinstar Depths (Melee) has a brief interlude remixing the original Silence theme from Metroid. This version is also orchestrated in Depth of Brinstar, as part of the Smashing... Live! album.
In Metroid Prime, General InterWorld Elevator is very similar to the version heard in Super Metroid. However, the melody is excluded from this version, stripping the song down to just its harmonies. General Recharge seems to be a variation of the same note pattern.
Metroid: Zero Mission remixes the original theme, without the added harmony of the Super Metroid version. This remix is also played in Save Rooms, which were not present in the original game. It can be heard here: 
Metroid Prime 2: Echoes features multiple remixes of Silence, based upon the original version from Metroid. The first, titled Ele, is a slightly faster-paced remix heard when using elevators. This remix returns in elevator and item rooms in Metroid Prime 3: Corruption and Metroid: Samus Returns, despite Silence being completely absent from Metroid II: Return of Samus; in the latter SR388 Underground instead constituted as an item room theme. In this version, the main melody is very quiet and may be obscured by the ambient drone and/or sound effects. It can be heard here: 
This remix's ambience is also heard alongside Luminoth-themed instruments in Echoes, when Samus Aran is removing light from a Dark Aether Energy Controller or restoring it to a light one. (heard here and here) An alternative version in Corruption, internally titled G-Heya, omits the instruments and plays in Generator A and C in Base Sector Zero on Norion (heard here). In Japanese, "heya" (部屋) means "room", with the "G" presumably referring to the Galactic Federation.
Metroid Prime Pinball features a remix of Silence on the Options screen. This version's instrumentation is nearly identical to General InterWorld Elevator, but the harmonic notes are absent while the melody can now be heard. It can be heard here:  Additionally, an ambient theme seems to consist largely of the low droning from Silence.
In PLAY! A Video Game Symphony, Silence is heard twice in the Metroid arrangement. This theme's eerie tone helps contribute to the dark mood of the medley.
Boss Go and Boss Mae
Echoes introduces another remix of Silence, a slower and darker version known as Boss Go. As the name implies, it is heard after defeating a boss (except for Dark Alpha Splinter, Emperor Ing, and Dark Samus 3 and 4), leaving behind a power-up for Samus to collect. Boss Go is also heard in Samus Returns, briefly playing after Metroids and other bosses have been defeated (including Movie Ending, after the defeat of Proteus Ridley). In the Queen's nest, it continues playing indefinitely after the Queen Metroid is killed, therefore also playing in the cutscene where the baby hatches. It can be heard here: 
Additionally, an abridged version of Boss Go is heard in both games, known as Boss Mae. It should be noted that "mae" (前) is Japanese for "before". This version does not feature the melodic notes from Silence. In Echoes, Boss Mae also plays during the introduction cutscene; when entering the Torvus Bog for the first time; between the Chykka Larva and Adult battles; and before the Quadraxis battle. In Samus Returns, Boss Mae plays in Area 3, where Samus inadvertently awakens the Diggernaut. Boss Mae is used at the end of the game's Overview Trailer as the game's title and release information is displayed.
All versions of Boss Go and Boss Mae were composed by Kenji Yamamoto.
In Metroid Prime Hunters, a remix (arranged by Lawrence Schwedler) plays after defeating a boss, and in the Alimbic Cannon Control Room. It is also available as track 15 in the Music Test and in the internal BGMSELECTLIST.DAT file, this theme is named Aftermath. It is arranged similarly to Boss Go, albeit with lower-fidelity instruments and compressed audio. It can be heard here: 
- The melody is notably similar to the Westminister Quarters, the chimes commonly associated with clocks such as Big Ben.
- Despite being heard in so many games in the franchise, Silence has never been included as a solo track in a soundtrack album ever since the Japan-exclusive Game Sound Museum: Famicom Edition 12 - Metroid, nor has it been included in a Soundtrack Gallery that gives names to tracks. Therefore, Silence has never been given an official English title outside of internal filenames.