When Link first enters the Southeast Quadrant and tries to dock at Goron Island, clouds will cover the sky and the Massive Eye will appear. The enemy resembles that of flying black whale. The enemy has as set of three eyes on each of its two sides. Link will need to shoot each of these eyes twice with his Cannon. The eyes will initially be yellow, but after one hit they will turn pink, and will then close shut after a second hit defeats it.
Throughout the battle the Massive Eye will shoot balls of energy out towards Link which can be destroyed with his cannon. Additionally, the Massive Eye will send out Eyeball Monsters flying towards Linebeck's Ship. Lastly, the Massive Eye will occasionally drop down to the water level and ram right into your ship, which is a completely unavoidable attack that deals a heart of damage.
The Massive Eye is defeated after all six of its eyes have been struck twice with the Cannon. Upon being defeating, the skies will clear up and Link will be able to dock at Goron Island.