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I also don't feel like you necessarily thwart (or destroy) the Combine stronghold in City 17 - just the warping machine in which Breen is trying to escape.

I think you do.

Alyx and Breen both talk about how you'll bring down the whole Citadel if you blow the reactor, which is supposedly what your goal was in the final scene.

After you do it, Alyx starts to say something like "I wonder if we have time to get out of here?" but the big explosion begins before she can finish the sentence, and Gman freezes time and takes you out of there.

The assumption is that Alyx doesn't make it, she sacrificed herself (and I suppose Eli and the other scientist, too, whom you'd left downstairs) for the cause of the rebels.
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Tony Fabris