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Up Your Arsenal
Ratchet takes on Klunk in his Ultra-Mech form. The fight takes place on a moving hover train (meaning falling off is instant death). Despite his size, Klunk is very easy to defeat. He has all of Giant Clank's attacks and one of his own. His main attack is firing a barrage of missiles from his hands. His secondary attack is firing an energy bomb that creates a shockwave upon impact with the ground. When at low health, he'll use an upgraded version of the aforementioned energy attack wherein he fires multiple energy bombs. Throughout the fight, Klunk with hover around the train, alternating between the three attacks. The recommended weapons to use are the Miniturret Glove, Nitro Eruptor, and Shock Cannon. The Nitro Eruptor in particular deals decent damage to Klunk. Rinse and repeat to take down Klunk.
Secret Agent Clank
Klunk now serves as the game's final boss, the fight is much more difficult than the one in the previous game. Klunk is now fought by Clank. The recommended weapons for this fight are the Gadgetron Personal Delivery Assistant. and the Wrist Mortar. The fight begins with two stealth takedown sequences where you must press the buttons in the order they appear on screen for Clank to successfully take down Klunk (note that hitting the wrong button or doing nothing will allow Klunk to take down Clank, dealing damage). After this, Klunk will don the Kingpin suit to attack. The Kingpin will use his cane as a flamethrower, firing large fireballs. The Kingpin can also generate a tornado around himself to push Clank into the water surrounding the arena. Use the Wrist Mortar to damage the Kingpin. Once you deplete his health, Klunk will jump out the suit and attempt another takedown sequence. Simply do the same thing as before to damage Klunk further.
Now Klunk will summon a robotic suit of Dr. Nefarious to attack. Robo-Nefarious attacks by firing streams of energy, and energy blasts that create triangular, electrified pads on the ground, making it dangerous to walk on. Once you disable this suit, Klunk will jump back into the Kingpin suit. Simply attack with the Wrist Mortar to force Klunk out and initiate another takedown sequence.
With half of Klunk's health depleted, he'll now summon a robotic suit of Ratchet. Robo-Ratchet attacks with his crossbow, firing a bomb that creates a large shockwave of energy, and summoning flying Agents of Doom to drop acid bombs. Klunk will also change suits more frequently. Just simply rinse and repeat the above strategy to bring Klunk down for the count and win the game.