A Hopper Nest is a large organic structure used by Alpha Hoppers to shelter in. Two Hopper Nests are present in the Gateway Hall room on Bryyo, during Metroid Prime 3: Corruption. The nests are bulbous globs, and look similar to other flora on the planet, suggesting they may not have been constructed by Hoppers and instead merely adapted to suit their needs whilst they took refuge inside them. When Samus first visits the Nests, the Hoppers do not respond to her presence and remain inside. However, when she returns after defeating Rundas they release Alpha Hoppers to battle her. Due to their resilient exterior, Samus is unable to damage them with any of her weapons. Luckily, they never spawn 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 first revealed 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."