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The Separatist Sub-Carrier was an underwater carrier vessel.
The mini-subs would exit through tubes located on the underside of the carrier. This was a dangerous maneuver, as Galactic Republic SCUBA troopers could ambush mini-subs on their way out, and there was no way of turning back once a sub was racing through the launch-tube.
The Xi-Char provided the blueprints for the Sub-Carrier to the Trade Federation free of charge for not being able to figure out how to make the manta droid subfighter transform like the vulture droid.