Vaati Transfigured is the second of three final bosses in The Minish Cap. The eyes surrounding him have now become more attached to his body.
The first part requires you to shoot at his eight giant eyes with arrows. Watch out for him shooting bunches of purple spikes. The spikes can be destroyed for occasional arrow refills or hearts. He will also cause rocks to fall from the ceiling and shoot electric orbs at you. After four of his eyes have turned reddish-orange, you must clone yourself using the Four Sword in the same pattern as the vulnerable eyes. Once cloned correctly, you must avoid the dark spikes on the ground, along with the other obstacles, working your way to the vulnerable eyes. Once close enough to Vaati, swing your sword so all the vulnerable eyes are hit at once. If done correctly, the eyes will disappear and Vaati will fall down, vulnerable. Swing your sword wildly at his center eye to damage him. He will eventually get back up and his eyes will reappear.
In the second part of the fight, Vaati will be slightly more aggressive in his attacks and movements. The pattern of vulnerable eyes will also change, but the process is the same. Shoot his eyes with arrows until four are reddish-orange and vulnerable. Clone yourself to match the eye pattern and avoid all attacks and obstacles until you reach him. Hit the four vulnerable eyes simultaneously, and Vaati will become vulnerable again. Swing at his eye to damage him until he brings his eyes back.
In the third part of the fight, Vaati will be significantly more aggressive with the electric orbs and much more aggressive in his movements. The pattern of vulnerable eyes will be different again, but the process is still the same. Shoot his eyes until four are vulnerable, clone yourself to match the pattern of vulnerable eyes, slash the eyes simultaneously, and slash his main eye repeatedly.
In the fourth part of the fight, Vaati never stops moving around, but he is still just as aggressive with his attacks. Another new eye pattern is in place, but, again, the process hasn't changed. Repeat the process from the last three parts of the battle while avoiding his attacks and quick movements.
Once defeated, Vaati will exclaim of his godly power and unstoppable might. He will question his loss to a child, and explode into a cartoon-like puff. You will then be transported to the battleground of the first phase of the Final Battle. Ezlo will comment on your impressive work and the door at the top of the room will open.