Consciousness returns. Gordon and Alyx discover they've somehow escaped both the reactor explosion and the G-Man's malevolent grasp. Before they can ponder their miraculous survival, the crippled Citadel lurches back to life just long enough to initiate a self-destruct sequence.
So somehow, they were saved. I imagine they are either transported to another area of the Citadel, or to the ruined chamber itself. Either way they survived the explosion. But what about Breen? Obviously Gman did not save him, and so he was stuck, still, at the bottom of the spire within the now radiation riddled chamber. The large relay towers were collapsing into the chamber, there was the explosion and the outburst of all that energy - which is seeminlgy powerful enough to cause that massive cloud looming about the tip of the Citadel.
Discover what’s become of City 17, Dr. Breen, and the G-Man.
We've seen Alyx, Eli and Mossman, all alive and in perfectly good health - who were also all in close proximity with the reactor explosion. Discover whats become of Dr. Breen....obviously, something has happened to him. He is a brilliant villain, so I doubt he's bit the dust.
What will he walk away from the chamber with? Scars? Loss of limb? Mutated? I think Valve have more creativity and classe than to make him into some towering mutant or 'Mecha Breen'.
"Don't wade into the field, it will peel you apart!"