The Reef was a prison facility constructed on an island and used by Ape City for the incarceration of ape convicts. The only access to the prison was by boat to a water-level platform, from where a large timber stairway led to the main structure.

In the era twenty years before the arrival of Taylor, the Reef housed the political opponents of Councilor Tenebris and his conservative views, including Timon, Gallus and General Aleron. Timon and Gallus organised a prison riot to cover Aleron's escape, but were almost foiled by Tenebris' agent Ursus who was stationed at the Reef explicitly to monitor Aleron. Ursus burned the wooden stairway in an attempt to prevent Aleron's escape. Ultimately, Tenebris was killed and the political prisoners were granted an amnesty.

In later years Doctor Milo was imprisoned at the Reef by Doctor Zaius for his role in supporting Aleron's human insurrection, but was allowed the freedom to carry on his valuable scientific research from his cell. Soon after, the chimp radical Cadmus also spent time at the Reef before returning to Ape City as a seemingly reformed character.

The Reef was still in use for political prisoners by the time of the arrival of Taylor and Brent, in the last days of the planet.

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