Jack: Abandon ship. Into the longboat.
Gibbs: Jack... The Pearl!
Jack: She's only a ship, mate.
Elizabeth: He's right. We have to head for land.
Pintel: It's a lot of open water.
Ragetti: It's a lot of water.
Will: We have to try. We can get away as it takes down the Pearl.
Gibbs: Abandon ship. Abandon ship or abandon hope.
Elizabeth: Thank you, Jack.
Jack: We're not free yet, love.
Elizabeth: You came back. I always knew you were a good man.
*Elizabeth kisses Jack. Will sees them*
Gibbs: Prepare to cast off. There's no time to lose. Come on, Will. Step to!
*Chains click. Elizabeth has chained Jack to the Pearl*
Elizabeth: It's after you, not the ship. This is the only way, don't you see? I'm not sorry.
Jack: *smiling* Pirate...
*Elizabeth gets in the boat*
Will: Where's Jack?
Elizabeth: He elected to stay behind to give us a chance... Go!
* * *
Elizabeth is in love with Jack but it's going to marry Will. In her mind, the only way to stop loving Jack is destroying their relationship... by killing him...
Her last line, given the circumstances, has all the logic in the world...