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The Drake is very different from the ships in Pikmin and Pikmin 2 in design, as it appears to be more technologically advanced. The cockpit is also different in that it is capable of holding more people, and may also be used as an access hatch. The Drake has a base from which four legs protrude, containing green lights, a hydraulics system and several other hidden mechanisms.
Directly on top of the base is a round body, featuring red lights and several other unique characteristics. It holds the three captains, has a long antenna attached to the top, and harbors a small satellite from which a blue beam emanates to help collect and analyze objects. It appears to have a world map on the back side.
Soon after the discovery of PNF-404, the Drake was designed and built by Alph's grandfather exclusively for our hero's mission. It then picks up Alph, Brittany, and Captain Charlie before initiating warp-drive. As they arrive at PNF-404, something goes wrong as the Drake attempts to enter the atmosphere, and it ejects the three occupants onto the planet below, all of which who land on different locations on the planet's surface. During the crash, the Drake loses an important mechanism, the Cosmic-drive Key.
After landing in a pool of water, Alph regains conciousness to see a damaged the Drake overhead, struggling to land safely. The sight startles him enough to wake him up fully, and he begins exploration of the surrounding area alone. Eventually, he comes across the Red Pikmin and their Onion, and using their help, is able to recover his KopPad device and relocate the Drake, which was able to land safely.
- It is speculated that the S.S. Drake is named after the canceled "Character D" that was supposed to appear in the game. Seeing as Alph was Character A, Brittany was Character B, and Charlie was Character C, it's possibly Drake was the name for Character D, but the name was moved to a ship as a reference.
- At the end of the day in Pikmin 3, before entering the S.S. Drake, one of the captains looks to the others, giving him/her a nod, signaling them to know they are good to go.
The Drake appears in the background of the Wii U Pikmin-themed stage, Garden of Hope. It doesn't appear to have any other function on the stage, however. It is in the spot where a Waddlepus and a Burgeoning Spiderwort are in Pikmin 3.