Empire Deathstool

WARNING: INTENSE SPOILERS
This is the final boss of Pikmin: Sinister Incinerator. It is the incarnation of the creature that formed the Complex Parasite, but even its true form is difficult to conceive. The Evil Being had one command in Complex Parasite's brain at the time of creation: launch a stupendous counter-attack if any being is able to successfully kill the Complex Parasite. When the remaining party arrives at The End, a swirling mass similar to an atomic bomb going off is seen in the middle of the seemingly endless desert. The smoke from the explosion then takes the form of a Puffstool, solidifying into the Empire Deathstool. It looks like an older version of the Puffstool and it is the size of Emperor Bulblax in the first Pikmin game. It also has many more antennae/eyes.

The Final Battle
The creepiest thing about the fight is its sheer simplicity compared to all the other bosses you've fought through to this point. That doesn't mean it's easy, though. Brace yourself for a rough encounter- no special tricks will help you out this time, although spicy-spray usually seems to make things easier, doesn't it? Anyways, fighting it is actually similar to fighting Puffstools- get it to trip over due to the weight of its oversized head and then throw Pikmin at its struggling body. But like the Omega Progg earlier on, it possesses inexplicably powerful psychic attacks, so you'll have to avoid the typical columns of fire, bolts of lightning and such, all elemental hazards can be wielded by this foe. Because it is like a Puffstool, the Empire Deathstool can send out spores to turn your Pikmin against you. The problem with these is that the spores spread out in far-reaching waves. If you see the boss start to suck in energy for the assault, run as far away as you can. There's plenty of room in the desert. Keep this up and you'll have this form defeated.

Another Monster Inside
It's not gone yet. The Empire Deathstool may be the title of the boss, but that's not what it really looks like. The actual boss was using the mushroom body as extra defense. After you deal enough damage, the top of the mushroom will start to split and bubble a bit, splitting in a circle at the top. The top of the mushroom pulls down, revealing some disgusting fungus even further inside. Eerier still is the fact that the fungus has what looks like one slit that glows red- possibly an eye? This part's kind of a joke. It's as if the boss can't decide which form it wants to use. The mushroom body will waddle around in no particular direction. Because its lost its mind it can't use any psychic attacks. Just run in and throw Pikmin at its body and don't get scared away by that weird fungus thing at the top. It can't do anything to you.

The Last Form
After you've inflicted enough damage to the mushroom body it will be permanently immobilized. The inner fungus will no longer see a need for the puppet mushroom and it will burn its way out of the corpse to fight you. Stay clear of the scorching- the spores that fly out of the mushroom can produce all kinds of random nasty effects. Stay clear of the haze and wait for the last form to emerge. And nasty it is. It's pretty difficult to describe exactly what it looks like- but it has two large wings, no visible feet and a large head with a big slit that definitely contains an insane pink eye. Its form is pretty cloudy, but just because you can't understand it doesn't mean you can't fight it. In the middle of the storm where its body and limbs should be is a faintly glowing light. If you throw Pikmin precisely at the center of the light they'll latch onto an invisible target and start hitting it, damaging the boss. If you miss they'll be crushed in the storm. The boss itself has the same attacks that the Empire Deathstool had, only amplified so that each of its attacks is a cataclysm in its own right. It even has one more attack that even the Deathstool didn't have- an explosion that kills everything within the radius almost instantly after it uses the attack. It winds up before it releases this one, so you can run away and call back your forces while you have the chance. It probably has this attack to make up for the fact that it can no longer spore your Pikmin. If you keep attacking the target the creature will eventually shrivel away into the desert sands.

Check here to see how the story finally wraps up.

Pikmin: Sinister Incinerator Ending