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At the point when truth is firing the rings? If you have played this through then it will make sense otherwise it is quite a big plot point. Basically the flood realizes what truth is doing and it will kill him and so he helps Chief and the Arbiter to stop them. After truth dies the flood betrays Chief and the arbiter
During that level, the Prophet was about to activate the Rings to kill the Flood and pretty much everything else. And the Flood didn't really feel like getting vaporized, so they helped Master Chief and Arby stop the Prophet.