So I was recently blasting through the MCC cause i’m hyped for it commit to the PC and i was playing Halo 3 and it dawned on me why didn’t cortana blow up the ship to destroy High Charity like she said to Chief. Their is nothing in game to explain why or am I missing something.
I believe it was because the Gravemind started interfering with her. They had quite the conversation between H2 and H3 that was shown in an Evolutions short story.
The Flood probably disconnected the reactor before Master Chief got away, so Cortana never had an opening to do so.