There was no way to defend Bastion from the Prince of Nothing — not the city on the shores of the Mirror Lake, certainly, and most likely not even the castle itself. As a strategist, Morgan was quite adept at evaluating both the strength of the enemy and that of her own — therefore, she knew that her side was lacking. Achieving victory did not seem like a realistic outcome.
It was very likely that she had not been sent here to achieve victory, to begin with. Buying her father enough time to defeat Ki Song seemed far more likely of a purpose.
So, Morgan had done two things after returning to Bastion from Rivergate.
First, she had claimed the Citadel for herself to gain control over it.
Second, she went to a vast underground chamber hidden deep below the castle, in the heart of a stone maze very few people knew existed, and even fewer still were allowed to enter.