After Olimar and the four other Leaders left, the Pikmin were left leaderless. Although the total population when the Leaders departed amounted to over one thousand, the number had steeply declined in the weeks that followed. A few Pikmin would drown in a pond, others perished by fire. Other unfortunate Pikmin would get crushed to death or will perish to the natives who feed on the Pikmin. Although a few scraps of food would help bring numbers up slightly, the decline of the Pikmin civilization was inevitable.

However, one fateful day a red Pikmin found an unusual and rare item. It was a replica of one of the Leader's whistles, a silver pea whistle with a small engraving on the side. The engraving read "Capt O," but what was most interesting was the piece of paper written inside. The paper was written in a black ink, and read "This whistle is one of the first whistles that I got from my company. Keep it in the Onion as a reminder of all the things we have done together." The red Pikmin, however, could only read a few of the words. However, the red Pikmin was educated enough to understand enough to know that the whistle had to be carried back to the Onion at all costs. This Pikmin picked up the small whistle with relative ease back to the Onion in time for the sunset. The Whistle was absorbed into the Master Onion, but nothing happened. Sensing the imminent danger, this Pikmin crawled up the Master Onion to get into the safety of the gelatinous liquid which stores and heals Pikmin.

The Master Onion majestically ascended to the heavens, far from the darkened surface of PNF-404. The 200 Pikmin crammed into the flying root looked in awe at the shining whistle on its makeshift pedestal. The red Pikmin who previously got the whistle was named Roy, and he was the leader of the Red Pikmin and head of the United Pikmin Council. He contemplated the meaning of the whistle and began counting the number of Pikmin left in his regiment. Only 47, including himself, had made it through the day. Roy noted that the numbers had dropped only 4 today, but the story could be different for the other 6 species. Roy decided not to worry himself too much and rest for the next perilous day on PNF-404.

For the Yellow Pikmin, the outlook wasn't as rosy. Ray, the quick-witted and attentive leader of his species, found that his Pikmin had reached a population of only 23. Yesterday, Ray mused, he had around 42 living Pikmin under his command. Several Pikmin were eaten by a Spotty Bulbear when Ray misjudged the distance from the tree branch to the ground. Tomorrow will have to be a better day, and the food will have to be much safer. After Olimar left, Pellet Posies had become much rarer than previously, and Ray suspected that the growth of species previously kept at bay by the Pikmin themselves had rebounded to numbers previously unseen. Ray thought about his purpose in life before drifting into unconsciousness.

The following day, things went as normal as they could go. Several Pikmin had died already, but the blue leader Rana had found a patch of pellet posies that was relatively safe to harvest. A blue Pikmin had found a one-pellet as blue as itself and carried it back to the Onion. Upon arrival, the blue Pikmin looked in satisfaction as the nutrient dense nectar crystal was absorbed by the unusual tractor beam. However, one of the seeds fell out of the Onion with a plop, scaring this nameless blue Pikmin. While one of the seeds had a leaf and glided gracefully through the atmosphere, the other had a bronze-colored whistle resembling Olimar's on top. This blue Pikmin then hid from the unfamiliar sight. Could it be a leader? Had an enemy been born by mistake? The Pikmin went over to the sprout with a leaf and pulled. After much effort, the sprout came out with a cute "hi!". Next, the 2 Pikmin started pulling on the whistle sprout. A short period of time later yielded a blue Pikmin similar to themselves with a whistle on its head.

The 3 Pikmin stared at each other, contemplating the meaning of the sites they are witnessing. There were one bud, one leaf, and one whistle. Finally, the whistled Pikmin let out a shrill note and the other Blue Pikmin immediately understood and respected their colleague's power. The blue Pikmin with a whistled immediately ordered his comrades to follow him back in the general direction of pellet posy patch, seemingly by luck. After bumbling about for some time, the group reached the Pellet Posy patch.

Rana looked in surprise at the unexpected visitor. Realizing that this new Pikmin had the inherent ability to control others of its kind, Rana the blue Pikmin leader immediately ordered it to round up the Pikmin who weren't going to carry pellets back to the Master Onion. Sunset was still a long way away, but Rana needed to bring her Pikmin back to the Master Onion to minimize loss. The whistle Pikmin had larger petals and was slightly shorter than the male Pikmin in the party, so Rana realized it was a female. She called the Pikmin Wilma and sent it back.

Meanwhile, Roy and Ray were busy fighting vicious dwarf Bulborbs inside of a cave. Both were taking light casualties, but their management was good enough that they would gain more Pikmin than they had lost. In between battles, Roy commented,"Ya know Ray, with the good Captain Olimar we could fly over those blasted Bulborbs much higher and faster. Nowadays we have to slowly toss each Pikmin and hope they land on top of the enemy." Ray nodded and prepared for the last battle of the day.

Upon reaching the final floor, Roy and Ray looked in anticipation at the final boss of the dungeon. A mossy hill lied in wait in the middle of a sandy arena. "I've been around since Olimar first arrived. That's the Emperor Bulblax, and probably a very strong one too," said Roy. Ray widened his eyes. He hadn't been around until midway through Olimar's second visit, and even then he only saw the weak Emperor. Ray was prepared, however, and readied his regiment of Yellow Pikmin. A loud roar greeted the Pikmin and sent most of them into a frenzy. Ray and Roy frantically called back their troops just in time for all to avoid the slobbery tongue of the Emperor. The battle would be long and hard, but the rewards reaped would prove to be invaluable for the Pikmin.