In the beginning of the High Charity level of Halo 2:

Cortana: "That structure, at the center of the city... it's a Forerunner Ship! And Truth is heading straight for it! If he leads the Covenant fleet to Earth, they won't stand a chance. You have to stop him!"

Master Chief: "That Brute has the Index. And Miranda and Johnson. He can activate the ring."

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."

While Cortana said just like we did the Autumn's, I am unable to understand it.
In Halo: Combat Evolved, Master Chief detonated fusion engines of Pillar of Autumn physically by cracking engine's shield with grenades (or, rockets). So, this method is out of question for Cortana.

When it comes to using self destruct mechanism of ship, one needs the ship's commanding officer's authorization or his Command Neural Interface to initiate it. In the Two Betrayals level of Halo: Combat Evolved:

Cortana: "I've located the Pillar of Autumn. She put down twelve-hundred kilometers up spin. Energy readings show her fusion reactors are still powered up. The systems on the Pillar of Autumn have fail safes that even I can't override, without authorization from the Captain. We'll need to find him or his neural implants, to start the fusion core detonation. One target remaining. Let's take care of the final pulse generator."

In Amber Clad's commanding officer Miranda Keyes (& her CNI) wasn't there to authorize self destruct of In Amber Clad.

How was Cortana really going to detonate In Amber Clad's reactor? Or, am I missing some other ways Cortana could do this?

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    Well, the physical destruction was only because Guilty Spark stopped the programmatic countdown, so that itself isn't an issue - that technique was the backup plan originally. Cortana was probably referring to the plan of using the reactors as bombs rather than the particular technique of igniting them. That still doesn't answer how she could get Miranda's permission, unless she could broadcast using the Covenant speaker system that Truth uses and get verbal confirmation, but that seems like flimsy security protocol. – rsegal Apr 23 '13 at 12:26
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    Is it possible that she still possessed Captain Keyes' CNI? We don't see what happens to it after HALO: CE, and we know that Cortana can possess a quasi-physical item (the Index). It is also possible that the procedures for In Amber Clad's detonation were different, whether because of ship size, commander's rank, or something else. And given all the things we see Cortana hack through, are the fail-safes really that secure? – The Fallen Apr 23 '13 at 13:36

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