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The Vaporizer's long range and accuracy is the most effective method for taking out these ships. The Visibomb Gun is also useful if you can get close enough to destroy them. The Heavy Lancer can be effective near the bridge, where the ships will pass right over you. One other possible method is using the turrets at the area where you fought the Thugs-4-Less leader's mech-suit to destroy the ships.
One of the easier locations to complete this is after the first set of swingshot targets near the ship. Face towards the second set of swingshot targets and look up, slightly to the left. Every few seconds three ships should fly over in a row.
- Ratchet & Clank: Going Commando (first appearance)