Quote Originally Posted by Guardian View Post
He takes her out as the halo ring goes off she says "Its been an honor serving with you, John". Then next time you see him he puts her back into the ship before entering cryo

http://www.youtube.com/watch?v=VybS1C-4CAk
This.

Also, I was under the impression Cortana started her rampancy when she entered the Control room, totally lost it when Gravemind captured her and became metastable (I think that's the term they use?) after the chief saved her.