Final Boss: Vaati
Defeat Vaati, the final boss of Minish Cap, to rescue Zelda and bring peace back to Hyrule.
First, watch out for the fireballs that Vaati will shoot, if you get hit you start running and will be disabled a while. Once he's done a fireball attack, kill the two eyes circling Vaati. If you take too long, the eyes disappear and Vaati shoots a black energy ball that follows you slowly. Just roll out of its way until it disappears.
Once the two eyes are gone, an eye opens on Vaati's body and he's vulnerable, so hit him as many times as you can.
Now there will be four eyes. Stay out from below them because they will each shoot a beam downward. From the side you can kill one of the eyes as they do this. Continue to watch out for Vaati's fireballs and black energy balls, kill the remaining eyes, and try to hit Vaati when he's vulnerable again. Unfortunately he may teleport away, so follow him and try to attack.
After this, the eyes around Vaati are protected, and you must use the Gust Jar to draw away the shield. Defeat the eyes as usual once you've sucked away the shield, but be careful because now Vaati will teleport around the room and may appear right on top of you, so keep moving.
Once more Vaati returns with the shielded eyes, so attack him as you did the last time around. Eventually you beat this form, but you've got a ways to go before he's beat.
Vaati appears as an eye surrounded by small eyes. During this phase Vaati will move around making it hard to split, and will also shoot out spiky rocks, may cause rocks to fall from the ceiling, and will also shoot out balls of electricity that do a lot of damage and disable you for a second.
Four of the small eyes are vulnerable once you hit them with an arrow. Reveal the four vulnerable ones, then split in the shape necessary to hit them all at once. Once the eyes disappear, hit Vaati as many times as you can. If you're out of arrows, break the spiky rocks around to get more.
After a bunch of rounds of this, this form of Vaati is defeated.
Dark Hyrule Castle
You automatically go upstairs. Walk up to the altar (a spin attack won't do anything if you try before Ezlo speaks in front of the altar) and then do a spin attack to turn Zelda back to normal. The castle starts collapsing (sound familiar?) and eventually you're returned to the first room of the dungeon. From here you have to go down the stairs to the left and follow the path BUT before entering the courtyard (where the final showdown takes place) exit south for hearts, bombs, and arrows. Then you can go into the courtyard, and this time it's really the final battle.
Watch out for the balls of electricity Vaati shoots out. They are very fast, they cause a lot of damage, and they disable you for a few seconds. If you have split into four, then if a ball of electricity hits you, your clones are destroyed and you take damage.
Vaati will appear with two arms and four small eyes in front of him. After a few seconds, one of his arms will come out of the ground. Hit it with the Cane of Pacci to flip it over and reveal a hole. Shrink to Minish size and go inside. One of the eyes in here is vulnerable; it's the one whose pupil moves around. Keep hitting it until it dies, then exit and return to normal size.
Do the same for the other arm. You need to use the lantern to see inside. Kill the vulnerable eye, then exit and grow to normal size again.
Now that the arms are gone, Vaati will use the four eyes in front of him. He'll shoot many balls of electricity. If Vaati shoots out a black energy ball, you can get rid of it with the Gust Jar. The eyes will shoot out balls of energy.
Split up after Vaati shoots a fast-moving energy ball. While split into four, stand in line with the eyes and swing your sword just as the energy balls reach you. If you do it correctly, the balls of energy will fly back at Vaati and hit the eyes, which disappear. After that, run up and hit Vaati's body as many times as you can.
Repeat the process, and eventually Vaati will be gone for good.
Congratulations! You beat the game! Be sure to watch the whole ending, then save your game afterward. With the saved game, you'll be able to get the 6 new figurines available from Carlov (but only if you didn't get the Carlov Medal already) and will be able to get access to the last piece of heart, rupees and the sound test with the final battle songs included. Enjoy!