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- Dominion: Intrigue
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- Dominion: Seaside
Secret Chamber is an unusual counter; it doesn’t stop the attack, like Moat does, and Watchtower sometimes does. But it can render an attack useless (or even helpful), and nowhere is this more evident than Pirate Ship, possibly the most reviled attack in the game. Simply reveal the Secret Chamber, then replace the top two cards of your deck with non-Treasures (ideally, Victory cards). A Pirate foolish enough to continue with the attack will only help you, by discarding cards you don’t want.
Secret Chamber works even better against Thief (because the attacker does not have the option not to go through with the attack, and is thus forced to discard your Victory cards), but Thieves are weak enough that you can usually just shrug them off. By contrast, Pirate Ship is one of the strongest attacks in the game. Secret Chamber stands out as one of the few effective defenses against Pirate Ships that doesn’t involve clearing your deck of all your money (which leaves you desperately poor) or surrounding yourself with Moats (which leaves you clogged with terminal +Cards Actions).
Dominion Strategy 
This situation can also lead to interesting mind games – once the P. Ship player knows what’s up, they’ll start taking money, and this lets you start putting unwanted treasure back on top with Secret Chamber, until they wise up to your plans anyway…
I don’t understand what you mean when you say, “Thieves are weak enough that you can usually just shrug them off. By contrast, Pirate Ship is one of the strongest attacks in the game.” It’s the exact same attack…
Obviously, Pirate ship is a MUCH MUCH better attack card because of the benefits it can provide its user and the fact that it actually eliminates treasure from the game instead of just changing hands. This is coupled with the fact that generally people will buy multiple pirate ships and deplete your treasure even faster. But the attack is the same…
It’s technically the same attack in the sense that Moat and Laboratory are technically the same Action—but of course they do very different things. That’s what I mean: Thieves aren’t an effective attack, but Pirate Ship is one of the most effective. I wouldn’t open with Secret Chamber to protect against Thieves, but I would against Pirate Ship.
Putting victory cards there is often weaker opinion. You need to keep track how many pirate ships could be played by opponent(s). When you are sure that its last attack you should put a secret chamber/colliding terminal there, opponent will rather take cash and you are protected for next round.