*SPOILER ALERT* Well I think our favourite A.I is not dead I mean seriously you think walking back towards the holographic wall equals death no I think when the librarian took Cortana from the Chief the first time she only fixed part of Cortana's rampancy because she needed to also genetically enhance Master Chief to defeat the Didact I'm not sure what the librarian did to Master Chief but I'm guessing she made Master Chief immune
to the affects of the composer. You know how Cortana says It's already done in the ending cut scene I think she means that she has to be transferred to where the librarian is so she can fix her.