During the first hours of the Covenant Civil War, both the Swords of Sanghelios and the Covenant Loyalists tried to take the gardens. Special Operations Elites and Grunts dueled with Brutes for control of the garden. Later on, two Elite Rangers came to the assistance of the Separatist cause. In the events of the Halo 2 campaign level Gravemind, John-117 slew the Separatist and Loyalists forces alike, as the Separatists had yet to join the cause of the UNSC.
The area, although fairly small, was rather complicated and intricate. There were two hills on each side, and only one way to get to them. It was sometimes a difficult to find area, especially since the area was somewhat dim. In addition, there was a Jackal Sniper on the immediate right, which might be hard to spot.
It can be assumed that the Hanging Gardens were destroyed when the Flood invaded and took over High Charity, or if not, it is certain that they were destroyed along with the rest of High Charity at the end of the Human-Covenant war in the city's destruction on The Ark.