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Entering the Mountain
Once you have beaten all of the Shadow Mario chases (plus the Pinna Park Mecha-Bowser) in every world, the plaza will be flooded. Head to the area where you use the rocket nozzle to get to the area behind the Shine Gate (there is no point in collecting the rocket nozzle though). There is a hole in the mountain that used to be closed up. Remember? Well, there is your entrance, and Shadow Mario is standing right there. He'll run into the hole. Go in to enter the volcano.
Spikes and Fire
You'll find Corona Mountain is completely different from the rest of the places you've visited on Isle Delfino. It is a huge, lava-filled cavern with danger in all directions. You must get through several obstacles to reach Bowser.
The first obstacle is a series of platforms. Some are ablaze, while others are rigged with spikes. You must use the Hover Nozzle to douse the firey platforms, and carefully and quickly time crossing over to the spiked platforms. There is absolutely no room for error here; one false step into the fire, spikes, or lava will cost you a life. Some platforms are safe, and one has a 1-up Mushroom you can grab. At the end of the series of platforms, you can refill your water. However, you'll now be taking a tricky magma river down the cavern, using a mud boat.
Crossing the Magma River
Hop into the boat. To steer, shoot in the opposite direction to that in which you want to go. You can't hit anything, or you'll sink the boat and lose a life. You'll be going down the river with several rocks in the way. Steer around them by slowly shooting your Spray Nozzle. There are fountains in the river you can use to refill your water, but don't crash into them, either.
At the end of the river, you'll find a cache of blue coins and a big rock platform with a Rocket Nozzle box. If you want to get the coins, be careful and steer the boat to where you can jump and get them. If not, grab the Rocket Nozzle and get ready, because there's nowhere to go but up.
Into the Clouds
The only way to reach Bowser is to blast up right under the cloud-shaped shadow on the rock platform. You'll end up landing on a cloud of all things. Now, you must blast higher and higher up through a bunch of clouds. Another one up is here, but tricky to get. You'll find the higher up clouds are moving in a circle, and you must time your blastoffs carefully to reach them. Falling can damage your health. The highest clouds are moving in and out, and require good timing to reach.
When you blast up to the top of the clouds, you'll reach a dark red one. This one leads to Bowser.
Bowser and Bowser Jr. are at the end of the volcano in a floating, sprite-shaped, slime-filled hot tub at Corona's Peak Peach refuses to get in with the two, and sees the Grand Shine Sprite deep in the slime. Then, Mario arrives and angers Bowser and Bowser Jr. One last battle awaits...
The Final Battle
Bowser and Bowser Jr. will throw everything they've got at you so you can't rescue Peach. Bowser will shoot fire and splash the hot tub's slime at you, and Bowser Jr. will fire off Bullet Bills, along with homing blue ones. You can stun Bowser Jr. with the Spray Nozzle, but Bowser is untouchable.
However, there are five points on the hot tub that have rocket symbols on them. Stand on them and launch yourself into the air. When you go as high as you can, go into a Ground Pound and you'll come hurtilng down with rocket speed and smash a point on the hot tub. Unluckily, you'll trigger a deluge of slime and make part of the hot tub collapse. You must hurry back onto the tub before you go down with the rest. Then, you must perform Rocket Ground Pounds on the rest of the points. However, doing this is damaging F.L.U.D.D.! What'll happen if you keep it up? It looks like there's no other choice...
There is only one way to win this battle: collapse all five points on the hot tub. When you succeed, you'll tip over the hot tub and knock Bowser, Bowser Jr., Peach, and yourself out, along with the Grand Shine Sprite.
Mario and Peach will end up landing on the lone island outside Delfino Plaza. They're okay, but F.L.U.D.D. has sustained heavy damage. He asks if he was of assistance, and deactivates.
However, Peach tells Mario to look up, and they see the Grand Shine Sprite return power to the Shine Gate, and it brings the Shine Sprites back! Everyone on Isle Delfino is celebrating!
Meanwhile, Bowser and Bowser Jr. are floating out away from Isle Delfino. Bowser tries to tell his son that Peach isn't his mother, but he's already figured that out, and has one thing on his mind: fighting Mario again someday. Bowser likes his enthusiasm and is proud of him, but wishes to take a rest.
At evening, Mario and Peach are looking at the sunset when Toadsworth and the Toad Brigade appear with a fixed-up F.L.U.D.D., once again his old helpful and reliable self.
Then, F.L.U.D.D. says the last line of the game:
"The vacation starts now!"
You'll get to enjoy the credits, which show pictures of Mario, Peach, Toadsworth, and the Toad Brigade enjoying their vacation on Isle Delfino. Now that the isle is clean and the Shine Gate is back to normal again, Mario can have fun with his pals. He gets a little stir-crazy and jumps from the plane at the airport, and ends up falling and becomes very dizzy. Peach catches a fish, giving her a souvenir of the vacation. The Toad Brigade and F.L.U.D.D. check out Noki Bay and take a group picture. Toadsworth chooses to ride Pinna Park's roller coaster, and gets the ride of his life!
After the group goes on their adventurous vacation, they relax and head back to Mushroom Kingdom. However, Il Piantissimo seems to have found E. Gadd's Magic Paintbrush...
After you collect all 120 Shine Sprites, you'll get a picture of Mario, Peach, and the gang inside Hotel Delfino's Casino, with most of the residents of Isle Delfino in the backround.
Congratulations! You've finished the game!