The interior of the Collector Base seems to be composed of both organic and inorganic material. Inside, countless Collectors work on processing the genetic material and live subjects they have acquired for the purpose of creating new Reapers. Millions of stasis pods can be found within the station where captured organics are imprisoned and then broken down into raw material to be integrated into a new Reaper body.
In Mass Effect 2, the Normandy SR-2 under Commander Shepard attacks the Collector Base after most of the ship's crew are abducted by the Collectors. After fighting off several Oculi and destroying a cruiser, the Normandy forces a landing and Shepard's team breach the base. The team's progress varies depending on the choices made by the player throughout the game. Team members that have not been guaranteed as loyal or are ill-chosen for specific tasks during the final mission may die, and even the abducted crew members could die if the player does not engage the suicide mission as soon as it becomes available.
Just prior to the final boss battle, Shepard has the choice of either overloading the Collector Base's power matrix and destroying the entire station, or irradiating it so that its organic components and crew are killed but the technology is left intact for Cerberus to salvage. In Mass Effect 3, if Shepard had destroyed the Collector Base, Cerberus manages to recover the heart of the Human-Reaper that Shepard's team fought. If the base was spared total destruction, the Human-Reaper's brain core will be salvaged by Cerberus.