In the first stage of the fight, Ratchet cannot harm the machine directly, instead he must destroy the oncoming Robots that are attacking him. Mr. Zurkon and the Mag-Net Launcher work wonders in this and other parts of the battle. The VX-99 in the meantime will slowly make its way towards Ratchet, firing its lasers and destroying parts of the platform. Just keep away from the lasers until Azimuth fires his ion cannons and temporarily stuns the robot.
With the VX-99 stunned. Ratchet can use his hoverboots to jump onto the boss. Now the hard part begins. Each of the robot's tentacles are supported by an exposed bolt on the hull, and Ratchet must use his wrench to pull off all three. This is somewhat difficult as the boss wiil continuously fire its lasers at Ratchet, and that each bolt removed destroys part of the robot's hull, making it harder to dodge the lasers. When the boss stops firing, that is your cue to remove the bolt. After removing all three bolts. Ratchet will automatically jump back onto the platform where he'll be greeted by more Nefarious troopers. Take them out and Azimuth will appear with his ship, allowing Ratchet to swingshot onto it and fly back to the VX-99.
Now you come face to face with the head of the VX-99. It will promptly activate its secondary defenses: sweeping lasers that Ratchet must jump over. These can only be stopped by destroying the three generators around the dome. The Constructo Pistol is great for this objective. Each generator destroyed creates large visible cracks in the dome. Once all three generators are destroyed. Azimuth will use his ion cannons to shatter the dome, exposing the head. Now's your chance to really do some damage, preferably with the RYNO V. The VX-99's only attack is to fire energy blasts from its turrets. Once its health is depleted. Ratchet will have only 20 seconds to latch onto Azimuth's ship. With some patience, the boss will be defeated.