Mushroomized Mainbrain

The Mushroomized Mainbrain is an enormous robot corrupted by spores spread by the Puffstools. It is the boss of the G-Base and it must be defeated in order to save the President (who is actually the second-to-last treasure in the game!) The boss is defeated before the end of the game, but it is not listed in the Piklopedia because it is not native to the Pikmin planet. The Mushroomized Mainbrain and the various machines it controls- G-Pods, Drilling Diggers and the like were scrapped equipment left behind on the Pikmin Planet as space trash by the All-Devouring Black Hole Loan Sharks.

Pikmin: Sinister Incinerator's Plot
During the encounter with the Mushroomized Mainbrain, much of the game's plot is revealed. The G-Pod that deceived Hocotate Freight in the beginning of the game was acting under the influence of spores spread from the Complex Parasite, and it was not acting under the orders of the Loan Sharks as you might have expected at the beginning. The parasite's special spores (spread through dispersion of Puffstools, and subsequently Mushroom Pikmin) managed to corrupt and reprogram the scrapped instruments of the Loan Sharks that they'd cast to the winds, and the Parasite had the machines drilling holes into the depths of the Pikmin Planet in search of Dark Spores it could eat. However, during the events of Pikmin 2 when Olimar and Louie traveled underground, the Complex Parasite was made aware of intelligent treasure hunters from another planet, and sent one of its pods to lure them to the Distant Planet and then have them search for treasures once more in the hopes that they would uncover the Dark Spores for it, and they did. Then, using the President as bait, the Complex Parasite lured Olimar and Louie to the G-Base in hopes of defeating them through use of the Mushroomized Mainbrain, the most powerful machine of the lot. Once they were defeated, the Complex Parasite's Puffstools and Mushroom Pikmin would bring it the Dark Spores they collected.

The Battle on the 12th Floor
Once Olimar and Louie and their Pikmin forces reach the 12th and final floor of the G-Base, they'll spot the President in the center of the room. Suddenly, he'll be lifted up onto the back of a gigantic robot (homage to the final battle of Pikmin 2) and the robot will start to attack. It has a few different attacks you'll need to avoid- something you'd expect from a crazy scrap-metal mushroom enemy.
 * Oil Spill - The central hatch in the robot's center unscrews and a surplus of disgusting gunk flows out, creating a sticky, slimy pool around the robot which takes a little bit to wear off. Pikmin will get stuck in this ooze unless they are Black Pikmin.
 * Highly Flammable Attack - The robot heats up, and a fire is lit inside the part of the robot that contains the oily gas. The central hatch unscrews and an intense blast of fire shoots out, spreading wide in whichever direction it is launched. The flames die down after half a minute, but if the fire goes off in a pile of oil the oil will burst into flame, making it a veritable deathtrap to Pikmin inside.
 * Life-Support Breath - The robot's head breathes Hocotatian air. This function was intended to keep Hocotatian space travelers safe from poisonous airs like oxygen, but it has a reverse effect on Pikmin that get caught up in it- they'll be poisoned unless they are White Pikmin.
 * Short-Circuit Swat - The broken limbs of the robot are electrically charged at the ends and capable of shocking Pikmin that make contact with them. Only Yellow Pikmin are safe from this.
 * Stamp - The robot attempts to step on Pikmin with its feet. Don't try swarming this boss.
 * Turret Fire - The head opens up to reveal a blaster similar to a Man-at-Legs. You can confuse the boss out of this attack by running around it in a circle, which will make the gun jam- and the robot will be open to attack.
 * Control - The Puffstool growths all over the metal body will shudder and then release Pikmin-controlling spores like a Puffstool. When the fungus starts to shake, stay clear of the robot until the attack is done with.

Any Pikmin can damage the robot's metal body, but Purple Pikmin will finish it faster if they are thrown at it. The boss will take a long time to beat unless you take this risk, but your Pikmin will be quite open to any one of the boss' attacks. After its defeat, the robot will fall apart and the growths around it will shrivel up individually. Take the President to the Research Pod, then go and collect the last treasure from the Black Hole: the final Dark Spore that the Complex Parasite was searching for. That will complete your list of 300 treasures and you'll be able to go home. Of course, you shouldn't go home until you make sure that the threat of the Complex Parasite is forever neutralized - so that means that you've still got two large dungeons left to go.

Mushroomization
Usually, the term "Spored" is used to describe something under the influence of a Puffstool's spores. "Mushroomized" is used here in a reference to EarthBound- if the player was infected by a mushroom enemy, the disease was known as Mushroomization.

Portal- Kombat