The Seeker Missile is located deep within the Torvus Energy Transfer Station. To reach it, you'll need to solve a series of environmental puzzles, often involving manipulating water levels and activating ancient Luminoth technology. Once you acquire the Seeker Missile, you'll immediately be able to use it. To activate it, hold down the Missile button (Y on GameCube, or the Missile button on Wii) and target multiple missile locks simultaneously. Release the button to fire a volley of missiles.
The Seeker Missile is essential for opening doors with multiple missile locks, which are found throughout Aether. It also proves incredibly useful in combat against certain enemies or bosses that have multiple weak points. Practice using it immediately after acquisition, as you'll encounter several multi-missile locks on your way out of the Torvus Energy Transfer Station, allowing you to access previously unreachable areas and continue your main quest.