Operation: ECHIDNA

Following up on information gathered from Operation: TYPHON, Naval Special Warfare deployed SPARTAN-II Indigo Team to the Magog Asteroid Belt in order to infiltrate the base of operations for the Cygnus Liberation Front, assassinate key targets, and exfiltrate. Over two months of surveillance, the UNSC Prowler Hunters Arrow gathered ship movements and transmissions, sorting through them for anomalies, finally pinpointing the Insurrectionist base to a rough area in the asteroid belt. It was only with the capture of United Rebel Front personnel in Alpha Hydrae that the UNSC was finally able to pinpoint the precise asteroid used by the rebels, and begin Operation: ECHIDNA. Using this data, Indigo stowed aboard a freighter that passed through the area frequently, quessing correctly that it would dock with the hidden base.
Complicating matters was the coincidental kidnap and ransom of UNSC Red Cross/Crescent medical aide workers, compromising the mission. Not missing a beat, the Spartans alterred the nature of their mission - killing the guards, the Spartans evacuated the hostages, capturing a rebel freighter for the task, and resorting to their backup resort - a HAVOC nuclear warhead, destroying the whole base. The rescued hostages were subjected to memory modification procedures to preserve the integrity of Indigo Teams existence, but otherwise the mission was a complete success.
The operation was classified GAMMA TWO, available only to the UNSC Security Committee. As such, knowledge of it never reached the general military, and even the Office of Naval Intelligence was left baffled. As far as the New Jerusalem colonists were concerned, the rebels had moved on to more prosperous regions of space, and few were sorry to see them go. Regardless, New Jerusalem was invaded and glassed by the Covenant, rendering the operation a moot point - it is likely that the Covenant would have shattered every asteroid in orbit of the planet if they had so much as suspected its use as a base, and the pirates would have been killed anyway.