The Endeavor (Captained by Lord Cutler Beckett didn't fight back because Lord Beckett was stunned. I shall explain myself. If you remember at the end of The Dead Man's Chest, Norrington hands over the heart of Davy Jones to Lord Cutler Beckett Since that point, Lord Beckett has had control over The Flying Dutchman and Sir Jones. So, in the maelstrom the Pearl and the Dutchman are duking it out and at the end of the battle, Jack takes Will's hand and stabs the heart with it. He who kills Davy Jones is now Captain of the Flying Dutchman. Therefore, now Will is Captain of the Flying Dutchman and NOT UNDER Beckett's control. SO, he joins up with the Pearl and goes up out of the Maelstrom and towards the Endeavour Beckett is stunned that one: the Pearl got out alive, two: the Dutchman is now turning against him and Three: all his plans are going to ruins. and because he is so stunned, he can't give out any orders. Which is when the ship is getting blown apart by the Black Pearl and The Flying Dutchman and he mutters softly to himself, "it's just...good business"