The Nine created a prison after leaving the Crucible of Souls wherein he captured a number of the Doctor's companions, including Katarina, Jamie McCrimmon, Jo Grant, Leela, Margaret, Romana II, Adric, Charlotte Pollard, Liv Chenka, Helen Sinclair and Bliss.
He used River Song to give companions names before he hunted them down and placed them in cells, blocked off by temporal fields (although he occasionally moved Charley between cells, claiming that this was due to her paradoxical nature and his 'desire for accuracy'). The Nine claimed that he would return the companions once he had the full set, but showed little concern for the Web of Time as he took companions from various points in history, such as abducting Jamie from a time long after he left the Doctor, while taking Adric from a point about half-way through his time in the TARDIS. The cells also shifted the companions slightly out of phase with real time, making it allegedly impossible for the Doctor to find them as he would be unable to track them.
Each cell was secured by a reinforced glass wall and temporal shields that would cause the prisoners to age to death if they managed to break out of the cell. The prison was also patrolled by twelve drone sentries designed to shoot potential escapees with increasing levels of intensity, the first shot just being uncomfortable and each later one being ever more painful each time they shot a particular prisoner, although the Nine admitted that he didn't know what level of pain the weapons could reach before it became fatal.
However, River had actually been manipulating the Nine by giving him particular names as part of her own plans to stage a prison break, with most of the gathered companions having relevant skills such as warriors, mathematicians and scientists. When Charley, Liv, Helen and Bliss were left in a single cell, River convinced the Nine to take a trip to acquire Katarina, aware that the trip would be particularly difficult due to the limited time frame in which he could retrieve that particular companion. Using Liv's knowledge of technology, Helen's experience breaking codes and Bliss's knowledge of hacking computers, the three were able to access the central computer of the Nine's prison through the food machine in their cell, allowing them to take control of the drones and open the glass door of their cell, and Charley was then able to pass through the temporal shield because of her nature as a paradox so that she could turn the barrier off to let the others leave. The Nine returned with Katarina's coffin as they were attempting to release River from captivity, but he was defeated when he was psychically attacked by Katarina as the artron energy she had been exposed to left her mind active enough to distract him when he was trying to establish her identity with a mind probe. Once the other companions were freed, River took them back to their times in the Nine's TARDIS after erasing their memories, Liv and Helen waiting for the Doctor to rescue them after locking the Nine in one of his own cells. (AUDIO: Companion Piece)