This is referring to the boss fight on Oltanis Orbit, Gemlik Base, it's at the very end of the level. This boss fight sees you flying the fighter jet ship that Ratchet can fly, you are against Captain Qwark in his bigger, and better ship. For a Walkthrough see below:
It's not difficult to destroy his ship, but the fight takes a while to finish. The main objective is to shoot out the engines on his ship, so start off by shooting one of them. At first Qwark will just fire easy to avoid missiles, you can destroy them easily with the machine guns. Once an engine has been destroyed he will lay mines down, best way to avoid it is spin in circles or just shoot them. Destroy another engine and he will start firing missiles from both sides of his ship at you, avoid them by circling around or just shoot them. Keep shooting him and then he will activate his shield and run off, leaving elite jets for you to destroy. Just use the machine guns on them to take them out easily, avoid their shots the best you can. Now you are back fighting Qwark, you just want to fire everything you have at him to quickly destroy him (shooting any area on the ship will cause damage), keep doing that until his health reaches zero. Qwark will be seen falling to the planet below on the cut scene, boss fight is done.
Trophy will unlock shortly after defeating him.