Pikmin: Sinister Incinerator Ending

Death To The Deathstool
After the defeat of the Empire Deathstool in The End (Floor 32 of Worlds Beyond), the final, unintelligible form of the creature explodes, sending the entire, endless desert into oblivion. As the sands of the desert and the smoke of the enemy drifts away, Olimar, Louie, and the remaining Pikmin seem suspended in midair. Olimar alone sees what's left of the creature's core: a Mushroom Pikmin, looking no different from any other Mushroom Pikmin. It stares at him for a second before exploding not unlike a bomb-rock, leaving nothing behind. The sand and smoke clears away as the red sky around them turns a shade of dark blue. All of the sudden, the night sky feels like rushing water pushing them all upwards. Their vision clears a little better and they see the rocky walls of a cave around them with a faint light at the top. They somehow found a geyser that managed to take them back to the surface!

The final "Cave Results" screen flashes by as the geyser pushes them upwards. Did you save all of your Pikmin?

The Shaking Portal
Olimar, Louie and the Pikmin are blasted out from the treetop at The Portal. They drift downwards to the onions and the ship. Good thing they landed safely on the island and weren't shot out into the sea! The Research Pod immediately hovers up to Olimar and Louie, expressing concern about their conditions ever since it lost sight of them on the 30th floor thanks to the rockslide caused by the Complex Parasite. Before they can speak to it, the whole island starts to rumble heavily. Sensing danger, Olimar, Louie and the Pikmin retreat into the ship and onions and take off in a circle around the island.

An Ancient Contraption
The island splits in a circle, revealing a huge mound underneath, some large, slightly spherical object clearly untouched for many long years, caked in dirt. Then, the dirt mound bursts into color and a large flower opens up on top. It spins like a propeller, blowing away all the dirt and lifting the multicolored object underneath into the air.

Mysterious Onions
It's a giant onion. Olimar, Louie and the President (from the side of a cockpit) watch it fly away slowly before vanishing right in front of them. The onions disperse, flying somewhere across the sea. With 300 treasures collected, the President saved and the Complex Parasite destroyed, the ship takes for the skies, finally returning to Hocotate.

The End, and Final Notes
Exactly what that huge onion was is not explained. It might not even be a real onion. Whatever it was, it vanished into thin air, and for some time had been dormant beneath The Portal. Judging by the onion's position, the Worlds Beyond are actually contained within its hull! Therefore, the large onion is actually a portal to reaching the pocket dimension that contains the Worlds Beyond.

As it was revealed after the defeat of the Empire Deathstool, the creature was nothing more than a regular Mushroom Pikmin which found its way inside the huge onion at one point or another and managed to take root at the center of the Worlds Beyond, and in isolation, grew into the Complex Parasite by devouring Dark Spores. Now that the large onion has vanished into thin air, it is safe to assume that the Worlds Beyond are gone forever. Thanks to the Research Pod, all the Dark Spores have also been destroyed.

Hocotate Freight, as the Research Pod predicted in Pikmin 2, will remain prosperous and debt free until the end of time... probably.

The Empire Deathstool is absolutely gone. It won't be appearing ever again. It was just a strange, unseen subspecies of Puffstool, whose mysteries remain unexplained for now, much like the Pikmin, the onions, and many other things from the Pikmin world. It's up to the scientists and explorers to discover new things about these subjects.

That's why Olimar, one way or another, is destined to return.