The Atoragon is a mini-boss that appears near the end of the Story Mode, and may be encountered several times before if certain conditions are met. While significant in the Story Mode, it is not a playable character.
The Atoragon has several moves at its disposal, below is a list of the craft's various attacks:
One of its more frequent attacks is a powerful ramming attack, where the Atoragon descends from the sky and speeds forward in attempt to hit you with its drill.
Another of the Atoragon's more frequent attacks is a laser barrage. It will face away from you and shoot four small streams of lasers from the side of the ship. These lasers are fairly strong, and the barrage continues for a certain length of time. Standing too close can lead to a significant loss of health.
Missiles / Main Cannon
Lastly, the Atoragon can fire missiles that travel for a great distance, and it can shoot a green beam from near the top of its drill. While the missiles can home in on your monster, the beam only fires straight ahead. These two attacks are typically used in a combination assault.