"Clearly, this facility is in complete disorder."

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The Space Pirate Mother Ship is the enormous flagship of Ridley. It is also the mobile HQ for the Zebesian Space Pirates. It was seen in the Metroid Manga and in Metroid: Zero Mission, where it landed in Chozodia. It also houses the giant security drone fan-dubbed as Mecha Ridley, a safeguard created in Ridley's likeness to protect the flagship. The ship replaced the Space Pirate Flagship depicted in the Metroid Manga. In Metroid: Zero Mission, it makes it clear that the Space Pirate's mothership was destroyed on Zebes after Samus defeated Mecha Ridley and this would seem to imply that the remains of the ship is the Wrecked Ship of Super Metroid. However, when players wish to leave Chozodia using the Power Bomb to revisit the other areas in Zebes, they are able to access a section completely separate from the Flagship which is overrun with Zebes wildlife, and has a closer resemblance to Super Metroid's Wrecked Ship; this area is near the glass tube walkway located between the Chozo ruins and the Pirate Ship. Also, Zero Mission director Yoshio Sakamoto has dismissed the possibility of both ships being one and the same - during Zero Mission the player passes through an area that appears to be outside the Super Metroid Wrecked ship in Crateria, whilst the Mother Ship has not yet landed.^[1]

The flagship has two noticeable cutscenes. After Samus defeats Kraid and leaves his fortress, a cutscene shows Ridley receiving a distress signal, supposedly from Zebes, in the ship's bridge; the next shot in the cutscene shows the ship changing course and heading back for the planet. Once Samus enters Ridley's lair, the second cutscene plays and shows the ship landing and Ridley flying out with a screech.

The Flagship also comes with a fail-safe measure if it is ever infiltrated and the drone is destroyed. Upon the defeat of Mecha Ridley, the flagship will trigger a 3, 5, or 7 minute Countdown, depending on the set difficulty level, taking out any infiltrating person or battalion with itself in a massive explosion. This self-destruct system seems to be directly connected with the ship's security system.

In the Metroid Manga it is again seen as Ridley's flagship, fighting against the Federation Army Special Ops Battleship Vixin IV. Midway though the battle it tried to warp to Zebes but is stopped by Adam Malkovich in the Vixin IV, knowing that if it makes it to Zebes it would effectively put an end to Samus' Zero Mission. Eventually, Ridley is able to make it to Zebes with his ship, but Samus was nevertheless able to defeat him and eventually destroy the Pirate vessel. In Metroid Prime: Episode of Aether, Samus destroys a Pirate vessel that was attacking a transport and passenger ship, and reports that the "Space Pirate Mothership [has been] eliminated."

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