This will unlock after defating the final boss of the main game, you do not have to beat the extra stage for this. The method that I used was using the Lost Holy Sword skill (located through a breakable wall in the room with a save point closest to the teleport gate in Stage 5), which just auto attacks against either the boss or her projectiles (such as when she summons the emerald spam). Dodge her projectiles to get the TIME and MP gauges to refill, then stop time and stand still, just letting the sword attack her. She has 10000HP,and each time I did this from a full 160 point TIME gauge, she lost a fair amount of her HP (12 damage per sword strike). Whenever you are waiting for the TIME gauge to refill,the sword will just use MP instead. Due to the frequency of her attacks, I never found myself close to running out.
You could also use the Thousand Daggers skill (40 MP/TIME per use, located 4 screens up and 7 right of the teleport gate in Stage 2). This skill has a large amount of I-frames, and deals fairly heavy damage. If you choose this method, alternate between using it when time is stopped and when it isn't depending on whether you have the necessary MP or need to not get hit by an attack,or just want to hurt her.