Hopper Nests are large organic structures encountered on Bryyo in Metroid Prime 3. Samus Aran only saw one such nest, located above the entrance to Gateway Hall. This hive is always protected by Alpha Hoppers.

The nest is a bulbous glob, and looks similar to other flora on the planet, suggesting it may not have been constructed by Hoppers and instead merely adapted to suit their needs whilst they took refuge inside it. When Samus first visits the Nest, the Hoppers to not respond to her presence and remain inside. However, when she returns after defeating Rundas it releases Alpha Hoppers to battle her. Due to its resilient exterior, Samus is unable to damage it with any of her weapons.

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