Mushroomized Mainbrain

The Mushroomized Mainbrain is an enormous robot corrupted by the spores produced by Puffstools. It is the boss of the G-Base and it must be defeated in order to save the President. 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, such as 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 at 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 one might have expected at the beginning. The parasite's special spores 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  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 the 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.

Battle in the G-Base
Once Olimar and Louie and their Pikmin forces reach the twelfth 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 giant robot, which will start to attack. It has a variety of different attacks at its disposal, but doesn't necessarily use them in this order:
 * The central hatch in the robot's center opens and a surplus of disgusting gunk flows out, creating a sticky, slimy pool around the robot which takes some time to disappear. Pikmin will get stuck in this ooze unless they are Black Pikmin.
 * The robot heats up, and a fire is lit inside the part of the robot that contains the oily gas. The central hatch opens 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.
 * 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 detrimental effects on Pikmin that get caught up in it; they'll be poisoned unless they are White Pikmin.
 * 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.
 * The robot attempts to step on Pikmin with its feet.
 * The robot's head opens up to reveal a blaster similar to the one a Man-at-Legs has. Running around the boss in a circle will make the gun jam, causing the robot to be open to attack.
 * The Puffstool growths all over the metal body will shudder and then release Pikmin-controlling spores. When the fungus starts to shake, stay clear of the robot until the attack is finished.

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 this risk is taken, and Pikmin will be quite open to any of the boss' attacks. After its defeat, the Mushroomized Mainbrain 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.