The Ark was originally created to build Halos, gigantic weapons that wipe out all organic life in order to starve the parasitic Flood of life to infect. This desperate measure conflicted with the Forerunners roles as custodians of the galaxy, and so it was decided that the Ark would also preserve examples of doomed species destroyed by the Halo so they could be reseeded once the Flood had been eradicated.
The surface of the Ark was divided up into vast Refugia sections, twelve on the Central Hub and twenty across the large, petal-like Spires that extend out from the center. Each Refugia recreates the environments of common life-supporting worlds and separated by huge walls monitored by Sentinels to protect one ecosystem from polluting another. The Ark monitors and controls weather, temperature and even natural food chains in order to maintain the habitat.