All I have to say is . . .
The Manly Dead Guy (email@example.com) writes:
While reading the level transcript for High Charity, after the part where Cortana mentions that if the ring is to be activated then she will activate In Amber Clad's reactors; I was interested in that she says "that she doesn't want to chance a remote detonation" when the Chief goes to put her back in his helmet. This wouldn't make an awful lot of sense due to the fact that whether she is in his suit or in High Charity's systems then she would have to remotely detonate the
reactors on the ship.
This could in my opinion be one of the two things: the first (as has been mentioned before on this page) that she wants to stay on board the ship for some possibly malicious reasons or as I believe she may actually be telling (at very least partially) the truth. This may seem a bit rampant but, as we know from the level Gravemind the In Amber Clad has made the trip to High Charity and as Cortana mentions in the beginning of the level High Charity " ... 'gravemind', used us. We were just a diversion; In Amber Clad was always its intended vector". So from what Cortana has mentioned and the fact that we know "gravemind" himself is on High Charity we could gather that Gravemind sent the Master Chief to High Charity to help cause chaos on board the ship so that he (in some form or another) and a legion of his "men" could take the human ship to get on board High Charity.
During High Charity we see this fleshy goop over the walls, floor and equipment. As we saw in Halo:CE with Keyes this might mean the flood are taking control of the systems of the ship. If this were to be true then In Amber Clad seen in the beginning of the level crashed into one of the towers in High Charity could be in fact be emalgumated into the covenant systems by the flood (or more specifically Gravemind) thus bringing upon Cortana's direct connection to In Amber Clad.