Defeat Giant Klunk is a mission in Up Your Arsenal taking place in Metropolis, Kerwan. When Ratchet traveled to Metropolis to find Dr. Nefarious, he eventually encountered Nefarious, his butler Lawrence, while also finding Clank held prisoner. Ratchet was confused, until he realized that he was not teamed up with Clank, but with an evil clone, Klunk, created by Nefarious. Nefarious mocked Ratchet and teleported away, leaving Klunk to transform into Giant Klunk to fight Ratchet.
The battle takes place across a moving grav-train, with another grav-train flying in later. Giant Klunk has a similar moveset to Giant Clank, and his main attack is throwing bombs, which will leave a shockwave behind across an entire train's carriage. In between attacks, Giant Klunk will fly to another carriage, normally firing missiles mid-flight. All of Klunk's attacks are best dodged by side-flipping while strafing, though it is crucial to remain in the middle of a carriage most of the time, as a wrong side-flip can cause Ratchet to fall off the train.
As Klunk is constantly moving across the train, the best weapon against Klunk is the Annihilator, due to its damage, range, and speed. The Disc Blade Gun is also useful, but is slightly slower than the Annihilator, and while the Flux Rifle deals sufficient damage, it is much harder to aim. Either way, it is important to dodge Klunk's attacks while never falling off the train, as this can end the battle early.
Halfway through the battle, another train will arrive, with nanotech and ammo crates. Use this to reload on ammo, and continue to attack Klunk. He can now drop multiple bombs in succession from one attack, which can be dodged again by jumping over them. Keep firing and dodging until Klunk is defeated.
To continue to the story, simply return to the Starship Phoenix to be assigned the next mission, "Explore the Crash Site". However, when you get back to your ship, Operation: URBAN STORM is available for the optional mission "Destroy the robotic Tyhrranoid Forces". It is a good idea to board the Galactic Rangers dropship and compete in these missions for bolts; only one of them is ground combat-oriented, so it should not be a problem if you found the previous mission difficult.