Essentially you're going to whittle the boss down to about a quarter of health. A mini cutscene will happen and his head will be the only part where you can damage him.
So when his head is submerged your only way of hurting him is to have a metal weapon or a metal-beam weapon. Essentially anything where you are shooting a ball and chain. These are the only weapons that can pierce through the surface of the water to damage the boss.
Once you have his health low take control of the engine and have your AI control the metal gun. Fly as close as you can to the surface and your AI will be able to take out the rest of his health for the achievement.