The entire story is one for Nunnally since she's The Protagonist in this one.
Her many fights in the Mark Nemo.
In the last act, she delivers her "World of Cardboard" Speech as she, through SHEER FORCE OF WILL, stands back on her own two feet (which she never does in the original anime) AND opens her eyes once more. The fact that both her inability to walk and see were both rooted psychologically doesn't detract from the awesome.
Charles' coup d'etat. When Schneizel tries to use some bureaucratic nonsense to stop him, Charles just says "Screw you, I'm the absolute ruler now" and basically does what took most real-world dictators several years to pull off in one speech..