For me, it's a classic. The idea was that while in Halo's central computers, Cortana was somehow infected or corrupted by the flood. Thus the "Warning: Hitchhikers may be escaped convicts" title actually refers to whatever flood influence infiltrated Cortana.

She had you blow up the ring not just because she didn't want you firing it, but because blowing up the ring would FREE the flood.

That would have been amazing.