In Echoes, the theme is heard during various points whenever Dark Samus is present and/or nearby. It is part of the "Dark Samus Appears Part 2" medley of themes. It is also heard when Dark Samus attempts to steal Samus's Light Suit after being defeated in the Sky Temple Grounds at the end of the game.
Corruption features the track in various scenes involving Dark Samus, including her resurrection within the Colossus at the beginning of the game, before she ambushes Samus, Rundas, Ghor and Gandrayda on Norion, and each time she absorbs one of the latter three Hunters, after Samus defeats them. Its final appearance occurs when Dark Samus is about to fight Samus herself on Phaaze.
The theme can be heard here: 
|Metroid Prime and Dark Samus|
|Abilities|| Metroid Prime: Particle Wave Projector • Seeker Missile • Snare Beam • Ultrafrigid Beam|
Dark Samus: Bomb • Boost Ball • Charge Beam • Dark Echo • Missile Launcher • Missile • Phazon bullets • Screw Attack • Shrapnel Beam • Stealth field generator • Varia Suit
|Misc.|| VS. Metroid Prime (Spider) • Metroid Prime Battle • Dark Samus Intro • Dark Samus Appears Part 2 • Darkness • Escape • Dark Samus Biography • Dark Samus Gallery |
Dark Samus Rooms • Dark Samus in Super Smash Bros. • 04ε: Dark Samus