- last post: 01.01.0001 12:00 AM PDT
I think Dr. Halsey took Kelly to stop ONI/Ackerson from messing around with the Flood and possibly releasing them from yet another Halo installation.
If you think about it, Halsey didn't leave until after she had studied Cortanas info concerning the Flood.
Going by Eagles theories (the best I've heard so far), I think Halsey knew that ONI/Ackerson was up to something but she didn't know all the details - possibly studying the Flood (though I don't think she knew about the Flood until studying Cortanas detailed files). Given the fact that Ackerson has detailed files concerning Spartan DNA, I could see Ackerson attempting to use Spartan gene-manipulations with the Flood in an attempt to create some sort of new super soldiers to combat the Covenant.
Once Halsey read Cortanas files on the Flood and Halo, I think she put two and two together and took off with Kelly in an attempt to stop ONI/Ackerson for fear of them releasing the Flood.
This would explain how they could introduce another Halo installation and the Flood in Halo 2 - probably towards the end of the game (maybe even the very end).