Now that you have the Master Rupee, you have everything you need to visit the final boss and beat the game. However, like most everything in the game, the boss battle will require rupees. If you have any extra items, gems, or other trinkets you can sell for easy rupees in town, do it now. The more rupees you have the better. At least 150,000 is recommended. Also, you can finish mapping any unfinished maps you have to get even more rupees. The final boss can be beaten without taking a lot of rupees to the fight, however, it makes it harder to do so. Once you think you're ready, stop in your house to save, then head for the tower. Once at the top, walk up to the pool and tap it and watch the cutscene.
Uncle Rupee[edit]
Uncle Rupee will give you all of the rupees that you have thrown into the tower throughout the game. This should be in the neighborhood of 450,000 give or take. These will be added to the rupees that you brought with you to the battle. He will then ask you to give him your rupees. Type in 0 to deny him any rupees. He will then get angry and the fight will begin.
Round 1[edit]
Before the fight begins, the Great Fairy will tell you that you can shoot rupees using the touch screen. Simply touch the screen and Tingle will fire rupees in the direction of your stylus. To move around (rather slowly) use 
. Something important to know if this is your first time fighting Uncle Rupee is that, when firing rupees, you just hold the stylus down on the screen to fire the rupees in a machine gun fashion. Do not tap the screen repeatedly to fire as this will only fire a single stream of rupees which do minimal damage.
In the first round of fighting, Uncle Rupee will be sitting down in front of you. To kill him in this first round, the goal is simple: Fire Rupees at him until his life gauge runs out. When the fight starts, simply hold the stylus down on the touch screen between Tingle and Uncle Rupee and start pelting him with rupees. After a few seconds, he will send a bodyguard out to start shooting rupees back at you. Simply hold your ground and keep firing towards Uncle Rupee and the rupees you are firing will destroy the rupees being fired at you and eventually the bodyguard also. Just keep shooting towards Uncle Rupee during this time.
After you deplete his life gauge a little bit, he will send two bodyguards to get on either side of you and shoot you with rupees. Defend yourself! This is the key to defeating Uncle Rupee in all 3 rounds without depleting your rupees too fast. Do not keep shooting at Uncle Rupee when you are being attacked from the side, as being hit with enemy rupees depletes your rupees very quickly. Sometimes one undefended attack can take 50,000 to 100,000 rupees away from you. Never be afraid of using your rupees too fast by firing, as firing uses your rupees very slowly compared to the rupees you lose by being hit.
When the two bodyguards surround you, quickly switch from left to right and back repeatedly blocking the rupees being shot at you. After a few seconds, the bodyguards will be gone. Then, a table of food will be pulled between you and Uncle Rupee. When this happens, just stay in the middle of the screen and fire a steady stream of rupees straight towards Uncle Rupee. The plates will start firing rupees at you, but your stream of rupees will block them. When the table disappears, your stream of rupees will once again be depleting Uncle Rupee's life. Once his life gets depleted over half way, he will turn red and the bodyguards will perform a different rupee attack. Again, try your hardest to block any rupees coming towards you. Then keep hitting Uncle Rupee. One more attack he will throw at you is a double stream of large rupees with you in the middle. When this happens, just stop firing and concentrate on staying between the rupees without getting hit by moving left and right with the rupee streams. When they disappear, recommence firing. Repeat this strategy until his life gauge is completely depleted.
Round 2[edit]
The strategy in Round 2 is different. You can't injure Uncle Rupee by shooting him directly with rupees, so don't waste any trying. The attacks in this round come a little faster, but still aren't that hard to defeat. The main attack in this round is a cloud that will either cover the right, left, or top of the touch screen and shoot a solid rain of rupees towards you. When you see the cloud coming, quickly move towards the opposite side of the screen from where the cloud is heading. Before the cloud starts firing rupees, simple place the stylus straight between you and the cloud and your stream of fire should block most of the rupees from hitting you. Once in a while the cloud will ball up in the center of the screen and start spiraling rupees out. Just get into a corner and move your stylus back and forth blocking the rupees. These are the main attacks in this round. There are others, but the goal in each is the same, just block any rupees being fired at you using your beam of rupees.
After his cloud and other attacks, he will raise both arms and start charging an attack. When this happens, get ready and as soon as you see him fire his attack, put your stylus directly between Tingle and Uncle Rupee. Your rupee fire will start repelling the attack back towards him. Keep firing until it eventually runs into Uncle Rupee, damaging him. Each hit takes a lot of health away from him. Towards the end of the fight, his cloud attacks will come faster, but can be defeated the same way. Keep repeating this until you hit him 3 or 4 times with his own charge attack and you will be ready for the next round.
Round 3[edit]
This is the Final round. If you still have rupees in the hundreds of thousands, then you are in good shape. In this round, you can once again do damage to Uncle Rupee by shooting rupees at him, just as in the first round. When the round starts, immediately start firing at him. Keep firing at him any chance you get. The faster you kill him the better. His only attack is to come down and hit you from above. Your only defense is to get out of the way. The problem? Tingle moves very slowly. You must do your best to try to guess where and when he is going to come down. Keep moving left and right and hope you're far enough away when he does finally come down. Once you deplete his life enough, he will start getting harder to predict. He will even fake you out by coming down half way and then going back up. If you watch closely, his mustache will twitch indicating where he is going to drop (left or right). If he hits you, you will lose a good chunk of rupees. Towards the end of his life, he will turn red and go even higher before coming down on some of his attacks. These attacks cause you to lose even higher amounts of rupees. Just keep firing at him constantly while dodging him and if you can kill him before your rupees run out, you will have beaten the game!
If you die, you will get a Game Over and have to start the game from your last save point. You will probably have to fight him a couple times to get the hang of his attacks, but once you do, the fight shouldn't be too difficult.
After you beat him, enjoy the ending! You have just beaten one of the most abstract and cool Nintendo DS games!