The flooded cavern is one of the largest rooms in Crateria. It is located directly outside the Wrecked Ship's crash site in Chozodia, and therefore features numerous fragmented walkways directly leading to a Green Hatch (Super Metroid) or Yellow Hatch (Zero Mission) entrance to the ship. These walkways cross over a lake infested with Skulteras. In Super Metroid, Samus can cross the gaps between the walkways using her Grapple Beam.
In Zero Mission, Samus briefly passes through the flooded cavern during her search for the Power Grip in Crateria's Chozo Ruins. In Super Metroid, Samus can easily traverse the flooded cavern and access the Wrecked Ship after acquiring the Grapple Beam in Norfair.
The room is significantly larger in Super Metroid, now encompassing a surface area with floating rocks and a narrow tunnel maze that drops down into the lake below. This upper area cannot be directly accessed from the lake area, but instead through the upper doors of the Wrecked Ship. These additional areas are actually present in Zero Mission, but are no longer in the same room as the flooded cavern and are instead classified as part of the Chozo Ruins directly above the room.
In Zero Mission, the flooded cavern is entirely subterranean, with smooth blue rock walls in the background. In Super Metroid, the flooded cavern is open-air, with the sky visible from inside the cavern, and the lake stretching far into the distance. The destruction of the Space Pirate Mother Ship at the end of the Zero Mission most likely obliterated the Chozo Ruins and unearthed the Wrecked Ship, which may canonically explain the flooded cavern's more open nature in Super Metroid.
In both games, the flooded cavern connects to the entrance corridor of the Wrecked Ship. In Zero Mission, the flooded cavern connects to the elevator to Brinstar; and the Chozo Ruins on the surface of Crateria. In Super Metroid, the flooded cavern to another Wrecked Ship corridor; the Gravity Suit's chamber; and the flooded cave where Unknown Item 1 was formerly hidden.
- Missile Tank
- In both games, a Missile Tank can be found in the bottom left corner of the flooded cavern. It is in a hidden alcove within the lake, which can be accessed by breaking through a Fake Block (Zero Mission) or Bomb Blocks (Super Metroid).
- Missile Tank
- In Super Metroid, in the upper area of the flooded cavern. Samus must ascend the floating rocks and Trippers to find the Missile Tank hidden in the highest part of the left rock wall.
- Missile Tank
- In Super Metroid, in the upper area of the flooded cavern. Navigating the Morph Ball maze will yield a Missile Tank resting on a pedestal on the left side.
- Much like Crateria itself, the flooded cavern did not appear in the original Metroid but was included in the Zero Mission remake, strengthening its continuity with Super Metroid.
- A unique orange Geemer appears in the flooded cavern, but can only be seen from a small enclosed walkway connecting Crateria and the Wrecked Ship. If Samus is in the flooded cavern and tries to approach the Geemer's location, it does not appear.
- The flooded cavern is the only room in Zero Mission where Skulteras can be found.
- The flooded cavern is showcased in the attract mode of Zero Mission.
- ^ Metroid: Zero Mission: The Official Nintendo Player's Guide pg. 89: "If you're low on energy or expendable items, recharge at the Chozo Statue nearby, then roll left and drop into the flooded cavern."