The Chozo of Zebes, in the midst of a discussion about the X Parasites on SR388, found that a Metroid was reacting to something. Mother Brain's eye mechanism then appeared and stated that an unknown large object was approaching the Planetary Protection Shield. The flagship uses the gravitational field of a micro black hole to destroy the shield, so that they could conquer the planet.
P-1 in his interrogation states that the Pirate presence on Jigrad was only to distract the Galactic Federation so that the raid of Zebes could occur. Samus Aran, upon realizing this, disobeys orders and flies to Zebes, with two days to save the Chozo.
Although forced to escape, Samus, Mauk and Kreatz found that the mothership was blocking their escape. Kreatz had sent a distress signal ordering the Federation Fleet to "get the @!#$ out here." Not even a short while later, Adam Malkovich arrived, and his fleet destroyed the flagship, forcing the Pirates to replace it with the Space Pirate Mother Ship, and for Ridley, the flagship's commander, to seek revenge on Adam.
It should be noted that the tech behind the ship is not believed to be of Space Pirate origin, and the Chozo wondered who they stole it from.
|Space Pirate Vehicles|
|Large Spacecraft||Flagship • Mother Ship • Orpheon • Siriacus • Vol Paragom • Starship • Leviathan Battleship • Leviathan-class capital ship • Destroyer • Colossus • Marauder-class battleship • Plunderer-class cruiser • Dragüd's Ship • Doomseye|
|Space fighters||Zebesian Pirate Ship • Boarding Pod • Fang-class fighter • Missile Transport (Elite) • Pirate Warship|