Each area except for Magmoor Caverns has a main boss. You can identify them by the fact that they have their own health bar when you fight them. See the walkthrough for more information on how to defeat them.
- Space Pirate Frigate boss
This is the first boss in game, located in the main reactor. It is surrounded by rotating shields and fires acid from its mouth. Plug missiles and beam shots into its mouth to defeat it.
- Reward: None unless you count the satisfaction of knowing that you've kept the Space Pirates from unleashing this monstrosity on an unsuspecting galaxy.
- Chozo Ruins boss
Flaahgra is a large mutated plant that is the source of the poisonous waters in the Chozo Ruins. It is surrounded by four dishes that reflect sunlight and needs constant solar energy. Its roots are its weak spot.
- Reward: Flaahgra gives up the Varia Suit when it's defeated, which protects Samus from super-heated areas in Magmoor Caverns.
- Phendrana Drifts boss
Thardus is an experiment created by the Space Pirates who used Phazon on a group of rocks, but the Pirates gave up trying to pacify it since it became too dangerous. Thardus has the ability to control the weather, roll into a ball, hurl large rocks, and encase enemies in ice. It resides in a Quarantine Cave in the Phendrana Drifts.
- Reward: Defeating Thardus gives you the Spider Ball.
- Phazon Mines boss
The Omega Pirate resides in the Phazon Mines. It is an extremely large Elite Pirate which is able to become invisible and regenerate health. It is considered by many fans to be one of the game's toughest bosses. It attacks with its powerful hands, a Wave Quake Generator, and a Missile Launcher.
- Reward: Defeating the Omega Pirate gives Samus the Phazon Suit, which protects her from blue Phazon damage.
- Tallon Overworld boss
The fight with Meta-Ridley occurs above the crater in the Tallon Overworld. Meta-Ridley has two forms: a flying form and ground form, who uses a number of weapons and melee attacks. His weak spot is the gem on his chest.
- Reward: Defeating Meta Ridley allows you to enter the Impact Crater, the final area of the game.
- Impact Crater boss
The final boss of the game. It exists in two forms: the first being a spider-like creature with mainly projectile attacks. This form is weak against Power Beam if yellow, Wave Beam if purple, Ice Beam if white, and Plasma Beam if red. The second form being a hovering, ethereal tentacled entity, sort of like a clear blue squid with bright menacing yellow eyes. Stand in the pools of Phazon it creates and blast it with your new Phazon Beam.
- Reward: Since this is the final boss your only reward is to watch the final credits knowing you've completed a very challenging game.
These creatures can be found guarding the various upgrades you need to complete the game.
A machine housing a hive of aggressive wasps it uses to defend itself.
- Reward: The Rocket Launcher
An armored beetle which is very aggressive and impossible to harm unless its back is turned. This creature appears as a random enemy later in the game.
- Reward: The Morph Ball
The main function of this machine is to burn the trash, but it will defend itself with jets of fire when challenged, and enlist the aid of deadly wasps as well.
- Reward: The Morph Ball Bomb
A boss in Phendrana Drifts, it's grey with spikes on its back that attract beams. You find it in the Chozo ice room. You can find baby Sheegoths in Phendrana shorelines. The Sheegoth itself appears as a random enemy later in the game.
- Reward: Defeating the head Sheegoth gives you the Wave Beam.