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.
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.
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 to beat it, then exit and return to normal size.
Do the same for the other arm, except now you'll need the lantern to see inside there. Beat 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 a lot of balls of electricity so take caution. If Vaati shoots out a black energy ball, you can suck it away with the Gust Jar. The eyes will shoot out balls of energy.
Your goal now is to split into four (try to time it so he's not about to shoot out the fast-moving balls of electricity), then stand in line with the eyes and swing your sword just as the balls of energy reach you. If you do it right, 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 much as possible.
Repeat the process, and eventually Vaati will be gone for good.
Congratulations, you beat the game! Be sure to watch the whole ending, because once it's over it lets you save your game. With the saved game you'll be able to get the 6 new figurines available from Carlov (provided you didn't get the Carlov Medal already) and will be able to get access to that last piece of heart, the rupees and the sound test with the final battle songs included. Enjoy!
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