Cortana: "If he does, I'll detonate In Amber Clad's reactor just like we did the Autumn's. The blast will destroy this city and the ring. Not a very original plan, but we know it'll work."

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Here's something I've just been thinking about: Given that Cortana couldn't really know, let alone anticipate, the events that were taking place inside Halo's Control Room (Arbiter and Johnson etc.), why did Cortana not detonate In Amber Clad's reactor as soon as Master Chief was clear of High Charity aboard the Forerunner ship?

High Charity was Flood-infested by this point, or at least getting that way. There was a high priority target in the Gravemind present and destroying the Halo could also have removed Truth.

Could the Flood have locked her out of In Amber Clad before Chief got away? Or was Cortana adopting a 'wait and see' attitude (fairly illogical given the pros of destroying High Charity) though if this was from self-preservation, then it could make sense (at least from her perspective!)