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Once the sun falls, you are beset by predators!
Your hypothesis about the large creatures on this planet being mostly nocturnal seems to be the case. The many predators and creatures of the planet come active at night; and they are ravenous. Even if you hid all your Pikmin inside the onions and you within your ship, you get the feeling the creatures would still attack- if not out of curiosity, then from the subtle smells of the onions themselves.
You decide to make use of all the types of pikmin available to you- a collection of all the colors with a few less green simple because they aren't fast enough for what you need- a few more red here for offense, some purples for weight, and of course orange for the flying creatures...
Attacked by giant crabs, wallywogs, and large bulborbs now active- you also employ several useful tools you've acquired from the various dungeons. You instruct some orange pikmin to grab some bomb rocks from a nearby deposit while spraying bitter spray on some of the creatures to stun them, while using spicy spray to empower your pikmin. Perhaps the biggest help of all is your Spudmin; huge and indomitable, it acts a bit like a big brother to the other pikmin- preferring to save them from the clutches of the various creatures instead of focusing on pure offense. Perhaps something it inherited from you?
Eventually, mercifully, you manage to hold off the creatures long enough that your ship can free itself with its now-unlimited energy source. The anti-stuck protocol pings you to return a few hours after sundown. You return to the ship, and along with them, the pikmin return to their own onions and you blast off for the rest of the night.