When Samus encounters it, it will swim around the room, entering and exiting four holes in the wall. It will sometimes poke its head out of a hole and spit green spores in a buckshot-like spray; these spores can be destroyed for pickups. Apart from this, its only means of attack is colliding with Samus as it passes between holes.
To defeat Botwoon, Samus must fire Missiles, Super Missiles, or Charge Beam shots at its head; the rest of its body is invulnerable. As it incurs damage, its red color scheme will become more intense, and it will speed up, making it harder to hit and avoid. Once Botwoon has been defeated, it will stop slithering around, and chunks of its body will rapidly fall to the floor and explode. Botwoon's death opens up the right wall so that Samus can continue exploring Maridia.
- Botwoon's boss theme is first heard during the battle with a minor boss from Brinstar: Spore Spawn.
- Serris in Metroid Fusion is also a sea serpent and swims similarly to Botwoon. The Fune and Namihe in Metroid: Other M are also giant worms that stick their heads out of walls to fire at Samus.
- It is possible to fight Botwoon from the other side of its chamber by performing the Spacetime Beam in the large room two chambers prior to Draygon (the one filled with quicksand and Mochtroids ) and then returning to Botwoon's room.
|Color||HP||ATK||E||BE||M||SM||PB||Maridia. Mini-boss. Shoot Missiles at its head when it appears.|
|Tallon IV||Aqua Reaper • Aqua Sac • Chomper Fish • Fish • Jelzap • Tangle Weed • Tallon Crab|
|Aether||Blogg • Bloggling • Alpha Blogg • Fish • Brizgee • Dark Blogg • Grenchler • Hydling • Krocuss • Phlogus|
|Dark Aether||Chykka • Dark Blogg • Dark Grenchler • Dark Phlogus • Dark Shredder • Flying Ing Cache • Venom Weed • Watchdrone|
|Zebes||Botwoon • Bull • Cacatac • Choot • Draygon • Evir • Gadora • Gamet • Oum • Owtch • Powamp • Puyo • Sciser • Skultera • Tatori • Tatori, Jr. • Yapping Maw • Yard • Zoa|
|BOTTLE SHIP||Fish • Skultera|
|BSL||Evir-X • Gadora-X • Owtch-X • Powamp-X • Mermen Pirate • Sciser-X • Serris • Skultera-X • Yard-X|