Flying Pikmin are kings in this level, and it should be one of your focus to get as many Pink Pikmin into the air as soon as possible, even at the detriment of the Red ’min if need be.
Remember to leave a Captain on idle duty at the Onion.
You could actually work more efficiently by setting Red Pikmin on the nearby Gold Piles more towards the end of the day, when the Pink Pikmin are clearing the Fruit from other areas.
You don’t need to use any of the colour change flowers in this level.
Another sneaky idea is to have Pink Pikmin take fruit close to the Onion, dropping it on the ground around the Onion, then calling them to another piece of fruit. Then use Red Pikmin around the Onion to complete the transfer. Factory line gathering.
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