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The ancient skiff is a space skiff on the planet Bion. It appears in Metroid Prime: Federation Force. M16: Slipstream on Bion sees the Federation Force landing on this skiff to investigate a message broadcast originating from it. General Alex Miles notes that the transmitter does not appear similar in design to other mechanisms found on Bion. He also states that it is possible the skiff runs along a rail system that the ancient Bion race used to transport goods between their cities.
A Pirate Warship attacks the skiff, destroying the transmitter. A countdown of 9 minutes begins and the Force is required to destroy the Warship before it collides with the skiff, killing the Federation soldiers.
The skiff has a defense mechanism where launchers will appear on top of it containing spheres similar to those "seen elsewhere on Bion", according to General Alex Miles. To attack the Warship, the soldiers must shoot the spheres off of the spawners and carefully shoot them into catapults at the helm of the skiff, much like in Blast Ball. The catapults will launch at the Warship and damage it.
There are three of these launch points, with gaps in the floor of the ship making it harder to shoot the balls into the catapults as they can easily fall off the skiff. There are also two other, different launchers near the helm of the skiff that cause the soldier using it to bounce to the back of the ship, similar to a Jump Pad. The skiff will give warnings about incoming bombardments and status updates on the speed of the Pirate Warship. After the Warship is destroyed, the Federation Force's ship arrives to extract them.
Following the battle, Miles remarks that the Pirates activated the skiff to lure the Force to their presumed deaths, and apologizes to them for failing to notice it was an obvious setup.