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Your best guess.
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The only means that high Charity could have gotten to the Ark is through the portal at Earth, and we know that High Charity was headed there anyway. The issue is that High Charity cannot possibly fit into the Ark portal because it's over 3 times its size, and the idea that the Gravemind would leave Earth entirely untouched by the Flood when he could've easily taken over the entire planet in a matter of hours is absurd.