- last post: 01.01.0001 12:00 AM PDT
I don't think that the Covenant and 343 would ever really become allies of any sort. If anything they would strike a deal. It is more than likely, however, that the Covenant simply captured Guilty Spark as a means to find the coordinates of Earth.
They also could have promised of helping to retrieve the key but who knows... Like I posted before, the status of the key/Index is completely unknown. As far as we know Cortana could only teleport it to another part of the ring where, when the Autumn detonated, it got destroyed.
Maybe 343 is upset over not being able to set into motion the wiping clean of the galaxy, or the destruction of his installation and many of the records with it. Maybe for 343 it is purely a revenge deal and he seeks to destroy humans. Perhaps if a deal was struck it was done on the idea of accomplishing a common objective.
However, maybe after everything gets set in motion 343 decides he wants to wipe all life clean still, because, after all, he is quite insane. This could be where the new Halo comes into the story.