Fly Pods appear to serve as a hive for different creatures, depending on location, spawning Reos in the Biosphere and Main Sector, Mellas in the Pyrosphere, and Himellas in the Cryosphere. All three species are related, hence why they share the same type of hive.
Fly Pods are usually mottled in red and green leaf-like patterns (perhaps a form of camouflage), although they are also sheathed in fire in the Pyrosphere or encased in ice in the Cryosphere. All variants are immune to the Power Beam, but they are all vulnerable to the Plasma Beam and Wave Beam, and all except the Himella hives are vulnerable to the Ice Beam and can be destroyed by three conventional Missiles or one Super Missile or a Power Bomb, excluding those that appear in the Pyrosphere, which are immune to missiles and vulnerable to the Ice Beam. The ones in the Pyrosphere contains a fire-like casing, which is only removed by ice particles. Afterward, they can be destroyed with the Missiles. Pyrosphere Fly Pods are easily the weakest of the three variations.
- There is one Fly Pod in the Main Sector that is hidden and spawns no enemies at all; rather, it hides a path to a Missile Tank. This expansion happens to be one of the earliest or final acquired expansions, and is near the top floor of the Bottle Ship Control Room.
- Fly Pods serve the exact same role as the War Wasp Hives featured in the Metroid Prime series and the Mellow Hives in Metroid: Zero Mission, which will continuously spawn flying insectoid enemies until their hives are destroyed.