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A Hopper Nest is a large organic structure used by Alpha Hoppers to shelter in. One Hopper Nest is present in the Gateway Hall room on Bryyo, during Metroid Prime 3: Corruption. 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 do 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. Luckily, it never spawns any more Hoppers on further visits.
Hopper Nests also appear in Metroid Prime: Federation Force on Excelcion, spawning Ice Hoppers. Trailers showed a health bar for the nest, which shows that these ones can be destroyed. A larger Nest is a boss in the game.
"Structure identified: Hopper Nest. The exterior is incredibly durable. Life signs detected within."