From the Super Mario Wiki
The Subspace Gunship is a giant ship controlled by Ganondorf and Bowser in the Subspace Emissary of Super Smash Bros. Brawl. It is far larger and more advanced looking than nearly any other ship in the game, with the Halberd coming close in size; the blueprints for the ship were based on technology used on the Isle of Ancients. It is also very powerful, capable of firing a beam that has the same effect as a Subspace Bomb and its smaller (relatively speaking) guns are able to tear clear through Halberd with a single shot, and have a very high rate of fire. The ship was built by the Subspace Army inside of Subspace, and was created as Tabuu's "trump card."
Role in The Subspace Emissary
After Ganondorf forces the R.O.B.s to send the Isle of Ancients into Subspace, it leaves a space big enough for the Subspace Gunship to emerge. Seeing the Halberd heading for them, Ganondorf initiates open fire. The Halberd initially avoids the incoming fire, but is quickly hit and destroyed in a single shot. Soon, Captain Falcon's Falcon Flyer, Falco Lombardi's Arwing, Samus' Gunship and Olimar's Hocotate Ship emerge from the Halberd's explosion and continue streaking towards the Subspace Gunship. The Subspace Gunship fires at the ships; however, they dodge all attacks. Busy trying to destroy the four ships, Bowser and Ganondorf do not notice Kirby on the Dragoon. Kirby flies through the ship with the Dragoon, causing it to break. Bowser and Ganondorf go through the Subspace portal right before the Subspace Gunship explodes.