It was protected by the High Charity defence fleet, which is supposedly the largest Covenant fleet in existence. Apparently High Charity could manage on its own though, since it is claimed to have enough firepower to destroy a Star. (How that would work, we don't know...)
It is also haunted by the spirit of a previous High Prophet, known only as Objection.High Charity was the epicentre of the heated battles that made up the Great Schism within the first few hours of the Covenant Civil War. After fierce fighting on both sides, the Station was severely damaged and the defence fleet had ripped itself apart as Brutes and Elites took control of individual starships and fired on one another. This meant that the Flood was easily able to infiltrate the station and infect the millions of Covenant that lived within.
When the Flood took over High Charity they completely altered its superstructure and used it as a mobile base for the Gravemind. It later crashed on the Ark and was utterly eradicated, save for the last vestiges of the Flood hive which took off into space, which was forever named Low Charity.