He begins the battle in his 'claimed by gix' form, but when he is defeated by a blast from the mightstone infused with power by a transcending Urza, he runs away and returns merged with his original Dragon Engine (the one he found in the dessert way back in the beginning of the story). It's been a while since i read it, but i believe Urza first thinks he rides on the back of the Dragon Engine, but mentally corrects himself when he realises that his brother is fused with the Dragon Engine through wires coming from both the Engine and Mishra. I believe Mishra is also completely mechanized by this point, apart from his face. I think it was left ambiguous if Mishra was still Mishra or if he had been completely replaced by a Phyrexian made to look like Mishra at this point.