Maybe I can shed some light on what may be happening. Note I had time to read ALL the novels waiting for this game to arrive.
The Librarian refers to Cortana as an Ancilla, this is the AI that the forerunners had in there armor.
When master Chief was "evolved" he began to hear voices from the Didact that Cortana could not hear, remember he asked her if she could hear it.
This would imply that Master Chief now has access to the "domain", basically a place where all previous forerunner spirits and knowledge exsists and can be accessed through lets say meditation. Its one way the forerunners retain knowledge for generations. Ancilla's help forerunners to access the domain and draw from the knowledge there.
In closing Cortana is quite possibly part of the domain now and I would say half way through the next Halo game she will be in full force with Master "Forerunner" Chief, not in Computer chip form but a part of his being.
