First, use the Bubbler to clear out the tunnel area as much as possible. Charge it up and kill the ones at the end as you walk past the area that triggers it.
Jump onto the treads and then back and forth between them about three times until it stops. Use a Level 3 Blade to hit the four weak points once and then run away, using it after that to destroy anything that comes back at you with the area-effect. Jump back on the treads again and repeat this until all four of the areas are gone. (It gets easier as they're destroyed)
When it stops, jump between the treads and fire the blade upwards. Press 'Q' and switch to Missiles, then fire as many of these as possible into it. If the Blade runs out, fire it again as it protects you from the homing fish missiles it fires at you. Substitute the Missiles for the Polar Star (Machine Gun or Snake if you traded early for either of those) if you run out, or a Level 2 Blade but then you aren't protected. It should die pretty quickly.
Poll