Paper Mario: The Thousand-Year Door Tips

Easier Way to Beat the Shadow Queen
The Shadow Queen is very difficult, and you may find yourself battling her for ages. A tip, is to stock up with 4 Lightnings, and 6 Ultra mushrooms. This way, when she gets her arms back you can attack all of her, and if she leaves you with barely any energy then you can recover!

I also suggest you have maximum HP, and FP, and use Vivian as an ally !