| I think you really need to go back to a save game before the eclipse attack or you won't be able to finish off the game. You probably had the Atton messege come up, but the game skipped it (like those flashy dialouges) and since you never responded to him, the action onboard the ship could not be triggered. I'm pretty sure this is your problem, since exactly the same thing happened to me.
The transmission does not necessarily come after the attack, that's just the usual case. You need to get the exchange mad enough (or pleased enough) to catch their notice, and that usually happens after the eclipse attack.
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Walk among them... these beasts that are less than you are. See their strength, see how easily you fall to their muscle and skill. Why do you stand for this, why do you submit to the flesh when death is bred in your bones?
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