Eventually, the UNSC Office of Naval Intelligence discovered the Covenant weapons smuggling, which was a major breach of the Cole Protocol. In response, an operation tasked with discovering the source of the Covenant weapons and halting the riots on Charybdis IX was authorized. A number of undercover ONI agents were sent in to spy on the rioters, Corinthia Hansen being one of them, and the UNSC light frigate UNSC Midsummer Night was dispatched shortly after. The ONI spies had discovered that the leader of the rioters, Jason Kincaide, had received the Covenant weapons from the Kestrel. After the riots were broken up, the Covenant arrived, following the smuggled weapons, and attacked Charybdis IX.
During the battle, Kestrel fled through Slipspace. After escaping, Kestrel made several more slipspace jumps, but Midsummer Night had secretly followed it from Charybdis IX. When Kestrel arrived at the Rubble, it inadvertently revealed the presence of the Rubble to the Midsummer Night . Shortly after its arrival, Kestrel docked in the Rubble. Later, its navigational data and all its electronics were disabled by an electromagnetic pulse created by a nuclear device used by Spartan Gray Team, although the hull and superstructure remained undamaged. It was presumably destroyed with the rest of the Rubble (save for Habitat Exodus) during the Battle of the Rubble.