Troy

From ILB

A human planet. According to memories revealed in the Phase 2 Operator's Monologue, Melissa intercepted Covenant command-and-control traffic that let the humans know that Troy was going to be attacked. 1st Lt. Sorenson was once stationed there, and Capt. Greene had family there at the time. A question was raised about whether evacuating the planet would reveal that the Covenant codes had been decrypted.

According to the Troy-related Axon Clips, at least some people on the planet were evacuated (http://www.thebruce.ca/ilovebees/TheAxons_Apocalypso.asp#sc1). Troy was glassed by the Covenant. The official story is that Troy was not evacuated (according to Miss Lawson, Rani's boss) and millions died.

What really happened is that Troy was partially evacuated, so the intelligence received by the Apocalypso did reach Earth. There was a cover-up of the fact that ONI knew about Troy, but decided not to act. Standish attempts to kill Rani for uncovering that Troy was partially evacuated. It seems that the Admiral did not know about the decrypt regarding Troy.

Spec is that the Pious Flea was a virus incorporated into the Covenant decryption. When Melissa decoded that transmission, she became infected.