Corrected entry: Where does Ace go after Joker electrocutes him? Batman jumps the Joker, and Ace just disappears until Batman carries Tim out of the building. In that time period you don't even see the pup in the background.
Corrected entry: Joker states that he inhabits Drake's body via a device with his DNA. However, Joker's appearance (green hair, white skin, etc.) was caused by a chemical accident. This would not have been imprinted into his DNA.
Correction: The Joker could have modified his DNA on the chip so that his "trademark" appearance would be carried over to Drake.
Correction: The scene is mainly focused on Batman and the Joker (Tim). Ace is definitely around, but not shown. He'd probably gaining his strenght/resting.