To defeat Otto (the final Boss), you need four weapons: The Optical Maser Array, Electro Rocket (with shock and Lock-on mods), Shield Barrier and the PDA. Put up a shield and use the Optical Maser Array to lower his shield. Then, blast him with the Electro Rocket. Keep repeating this until you defeat him. Use the PDA if you run out of ammo. This is when you and Otto are the same size, not for the Battle Ratchets, Giant Otto or the Giant Clank Battle.