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He didn't. Truth has no control over the Flood. Gravemind did. Gravemind was able to get a Flood-infested ship past the Elite blockade and sent it to Earth to stop everyone from going to the Ark through the Portal on Earth. The ship most likely was also a distraction so that Gravemind could get High Charity into Slipspace so he could get to the Ark wothout being follow.

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