Royal Combined Fleet of Sovereignty

In Halo 2, the fleet was seen throughout the campaign. When it exits slipspace above Halo, Cortana notes that it is the largest Covenant fleet ever seen. This is probably due to the fact that High Charity is the Covenant "holy city" and contains many things important to the Covenant. In Halo: First Strike, the fleet is described in the final chapter. A ship approaching High Charity had a nanosecond to submit a security code, or it would be destroyed by the sheer might of the fleet.

It may be the factual Second Fleet of Homogeneous Clarity, or it may precede or antiquate it considerably.

This fleet was completely disbanded in the Battle of High Charity when the Great Schism erupted in the Covenant. There was a large battle within the fleet, ending with most of the surviving Covenant Loyalist ships going to Earth, and the Covenant Separatist ships staying to attempt to contain the Flood. These attempts failed, however, when a single Flood Ship broke through, and headed towards Earth, with a small battle group of Covenant Separatist ships in pursuit.

Reformation and the Forming of the Fleet
The Loyalist ships that did survive regrouped at the Covenant Prophet's homeworld, with the total population being less than one thousand. The resulting fleet grew to an immense scale, larger than it's previous size, much larger, and the Covenant was reformed, making the base of operations the Prophet homeworld. Even with over 1 million ships at Earth, the majority of the fleet remained in defense of the Prophet homeworld.