Make sure that you have 60 HP, 60 FP, and 30 BP. When you fight her just as Peach use Vivian as your partner. Then. use the spinning jump and Vivian's Shade Fist until the Shadow Queen turns into her other form. Then switch to Koops. Use his power shell to attack the hands and the body. Then, use the Power Smash badge. Also, when she adds 7 more to her next attack, use either Koops' Shell Shield or Vivians Veil. Make sure both Koops' and Vivian's level is at the highest. Repeat this and you should be able to win. Do not forget to heal and make sure you have a lot of Life Shrooms.
This Boss has a maximum HP of 150. In her first form, she has a max attack of 7 and defense of 0. Use HP and FP Plus Badges and Power and Defense Plus Badges to have a better chance. When she reaches 70 to 80 HP, she turns into her regular form. She is invincible for four turns, then recovers all health. Then, a very long intermission sequence will begin and she will be attackable. Use emergency Sweet Feasts and Supernovas. Her hands are a force to be reckoned with; try using Admiral Bobbery's Bob-ombast or Vivian's Fiery Jynx if either is leveled enough. It may require a few short turns to learn to dodge her attacks. After some steady battling, you will defeat her.
This trick requires some attacking items, some recovery items for backup, Badges of any kind (Close Call, Mega and Power Rushes, and any others that are powerful and that can make your opponents miss more recommended), and Vivian. At the beginning, use up your attacks because your power will recover. When the Shadow Queen changes into her true form, use anything except items. After the intermission sequence and Peach giving Mario her power, do the following. If the Shadow Queen has her big hands, when it is Mario's turn use Power Smash or Spring Jump (recommended) on the Shadow Queen, and not the Hands. When it is Vivian's turnm use Fiery Jynx and that will kill the Hands. When the Shadow Queen uses her Dead Hands, have Mario either use Fire Drive, an item that attacks all enemies, Earth Tremor, or Art Attack. When it is Vivian's turn, have her use Fiery Jynx. This will finish off the Dead Hands. When the Shadow Queen boosts her attack and defense by three, have Mario use Power Smash. When it is Vivian's turn, have her use Fiery Jynx unless there are no Hands of some kind, then use Shade Fist. When the Shadow Queen does a Super Charge, have Mario use Power Smash, Spring Jump, an attacking item, or an attacking Crystal Star Ability. When it is Vivian's turn, have her use Veil. If Mario has low HP, then use an item or Sweet Feast. If Vivian is low, give her a weaker item such as Super Shroom or give her Sweet Feast or Sweet Treat. When the Shadow Queen gets low HP, have Mario use attacking items. Vivian should either attack, or use an attacking item, unless the Shadow Queen does a Super Charge. If that happens, use Veil. After all that, use Supernova and do a good job of it. Have Vivian attack then finish her off.