Dalamud (Read: Bahamut) had been drawing crystal energy for a while. This explains anomalous crystal formations and behaviors in and around Mor Dhona, but also goes along with why the Primals are so bent on having crystals in their possession. It seems to be their primary font of power (If you beat Garuda, there's a scene where as her avatar is vanishing, she reaches toward Dalamud and proclaims that the crystals are hers as you see the energy flowing from her and toward the moon). Darnus kept showing up and applauding the players for defeating the primal avatars, seemingly in mocking fashion, but it seems now that you were doing the dirty work for him. I don't think Darnus broke the seal himself, per se, more so helped increase the flow of energy to Dalamud and initiated its descent when the time was right. Bahamut was just bursting with energy and has, supposedly, had a few hundred years of captivity to seethe in rage.