Beyond beam weapons, Samus utilizes powerful explosives. Missiles are a secondary weapon, dealing significant damage to enemies and capable of opening missile-locked doors. They are a finite resource, replenished by pickups or at Save Stations. The Seeker Missile upgrade allows Samus to lock onto and fire multiple missiles at once, crucial for multi-missile locks and certain boss encounters.

Power Bombs are the most destructive conventional weapon in Samus's arsenal. Deployed in Morph Ball form, they create a massive explosion that can clear out large groups of enemies, destroy reinforced structures, and reveal hidden passages. Power Bombs are very rare and should be used strategically. Both Missiles and Power Bombs have expansions that increase their maximum carrying capacity, found throughout Aether.