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The Pikmin have never spoken to you, but they always seemed to understand what you wanted- until this. You tell them you are leaving. It's time for you to go. You can't live on this toxic planet. The SS Topaz is back to its full ability, and it's time for your flight.
You pull off the Braclet of Command and find it very elastic- enough to put it on Spudmin's wrist. He looks at it warily. Many of the Pikmin mull around him instead of you- though they don't seem aggressive as though you were a threat to their new "leader", they seem a bit split. You aren't sure what else you can do.
"Come on in the shuttle. I'm going to drop you off somewhere a little warmer before night falls."
With that- you and the onions take a short flight to a more southern hemisphere- going against the planet's rotation- as to gain daylight. By the time you find your destination, you know there will be enough time for them to be ready for night time. You head back to the first place you touched down on this planet- the placid crash landing site. With his sword and braclet, you leave Spudmin as the defacto leader of the Pikmin as you blast off- there is nothing left for you here now.
As you climb higher and higher into deep space, you notice worryingly that the onions you've collected along your journeys are following you. Just like every other night- but you aren't planning on spending your night in low-atmosphere orbit either. They climb into the stratosphere and high atmosphere- and then they stop. Unwilling or unable to go any further. You leave the planet's orbit and into deep space, take one last look, and blast off towards Hocotate. You managed to survive PNF-404, the Pikmin Planet, and are now finally heading home.