Kamek meets with Bowser,now in his Dry form,& introduced him to Wart. They begun making an agreement to have Mario destroyed & his potion will be making him whole again. They were reported by the Koopa Troopas,who informs them about Mario & Peach's vacation Plan. Bowser sent Wart with his secret weapon.
Mario,Peach,Toadsworth,& the other Toads went to Isle Delfino where the runway is covered in Paint like goop. Mario acquired FLUDD,a talking water cannon. After Mario cleans up the runway & collected a Shine Sprite,He was arrested for polluting their Island & the disappearance of the Shine Sprites,which he hadn't committed.
While Mario begin cleaning up the mess,He was confronted by a Shadow Blue figure that look like Mario,who was called Shadow Mario. He kidnapped & uses the magical paintbrush to escape. Mario realize that Shadow Mario was the one who framed him. After Mario retrieve 7 more Shine Sprites,FLUDD revealed that he was created by Professor E Gad,who also invented a Magical Paint Brush before it went missing until Shadow Mario has it. After retrieving the Eighth one,He was later confronted by Dry Bowser & Wart. After Mario defeats them,Wart summons Gooper Blooper to attack Mario,but he manage to defeat him.
Mario tries to retrieve the last of it,He was confronted by Shadow Mario,who transforms into Bowser Junior. Junior reveals that he was made from Bowser's DNA & He was sent to frame Mario. He pursues him to Corona Mountain where he was confronted by Dry Bowser & Wart. After Mario defeated Junior,Wart betrays Bowser & battles with Mario himself. After Mario defeats him,He freed Peach. As Wart gets back up,Dry Bowser,who was now dipped into Wart's Potion & became whole again,incinerated him with blue fire. Mario escapes with Peach,But Junior damage FLUDD.
The Shine Sprites return to their rightful owner and the Island is now restored. The people of Delfino congratulates Mario & repairs FLUDD. Mario & Peach went for an underwater swim & Toadsworth sips on a Pineapple Juice.
Mid-Credits: FLUDD tells Mario that he has a distress call from E Gadd,saying that Luigi has walked into a set up.