Plasm Wraith

The Plasm Wraith is the main antagonist and final boss of Pikmin 3. While scientific information about it is unknown, it can be presumed that it is a relative of another creature from PNF-404, the Waterwraith. It resides in the Formidable Oak where it obsesses over Olimar, which it holds captive. The Plasm Wraith has a wide array of abilities which include flight and various elemental powers (fire, water, electricity, and crystal). After it is defeated, it is revealed to be still alive, growing in anger from the top of its mound as the Koppaites and Olimar leave PNF-404.

Mysterious Life Form
The Plasm Wraith is liquefied in this phase, making it immune from damage. It chases after Brittany as she has Pikmin carry Olimar while Alph and Charlie find their way around the underground maze of the Formidable Oak. Pikmin are unable to damage it while it is liquefied, they just get stuck inside it, only able to free themselves once a Captain whistles on them.

Any enemy that comes into contact with the Mysterious Life Form is absorbed and killed instantly. If the Mysterious Life Form is able to get Olimar, it becomes solid and dashes for the entrance of the maze, with the day ending instantly if it manages to reach the beginning of the cave. All Pikmin stuck in the Life Form die instantly once it solidifies. It is avoidable by dealing enough damage to the Life Form, stunning it for a short time. Upon Brittany and the Pikmin carrying Olimar leaving the cave, the final battle begins.

Plasm Wraith
Upon ambushing the captains and the Pikmin at the bottom of the Formidable Oak and absorbing Olimar, the Plasm Wraith gains a physical body and the final battle begins. The Plasm Wraith attacks by creating needles from its "arms" and skewering Pikmin on them, before consuming them through the hole in its head. Rock Pikmin are immune to skewering, so they are the best choice while fighting the Plasm Wraith.

After enough damage is dealt, the Plasm Wraith shakes off the Pikmin, as well as pieces of its body. The Plasm Wraith absorbs the pieces it lost after a specific time, regaining health, but destroying the pieces will prevent it from absorbing them. After enough health is torn from its health bar, the Plasm Wraith will eject an elemental power made of pieces, which can only be destroyed by a certain Pikmin type: a fire pit (Red Pikmin), an electrical barrier (Yellow Pikmin), a giant water bubble (Blue Pikmin), or a crystal cube (Rock Pikmin).

The Plasm Wraith may also take flight and aim at the Pikmin on the ground, but can be slammed down by enough Winged Pikmin. After its health bar is fully drained, the Plasm Wraith will spit Olimar out before retreating back into the Formidable Oak.

Trivia

 * The Plasm Wraith has its own trophy in Super Smash Bros. for Wii U.
 * The Plasm Wraith is the only Pikmin final boss to survive.
 * Yellow Pikmin are the only Pikmin required to complete the Mysterious Life Form phase.
 * The Plasm Wraith appears in Super Smash Bros. Ultimate as a Neutral type Primary Spirit. It is only obtainable by summoning it using the cores of Hakkun, Eddy, and any Neutral type Spirit. While powerful, its ability decreases running speed.