Plasm Wraith

The Plasm Wraith is the final boss of Pikmin 3, and is the one responsible for capturing Captain Olimar. It is a virtually featureless, vaguely-humanoid being made entirely out of a golden cellular protoplasmic mass, which allows it to split different parts of its body off to create other semi-independent entities. It is fought in the Formidable Oak. Even if only one Plasm Wraith is seen in Pikmin 3, it can be considered as its own species.

Olimar's arrival
When Olimar first arrived at the Formidable Oak, he saw a gold, shiny substance at the top of the tower, and decided to investigate. Louie expressed discomfort and chose to stay behind, letting Olimar go on ahead without him.

Capturing Olimar
Olimar's stumbled across the Plasm Wraith during the his exploration of the Oak, at first, the creature was curious and playful towards Olimar and did no harm to him. However, when Olimar tried to leave, the creature became aggressive, triggering his suit's auto-sleep function and dragging him back to its cave. It became protective of Olimar to the point that it would attack anything that showed interest in him. The exact reason for this bizarre behavior remains unknown.

Rescuing Olimar
When Captain Charlie, Alph and Brittany reached the Oak with the hope of finding Olimar who found the Cosmic Drive Key of the S.S Drake, the only means for the Koppaites to leave PNF-404, they stumbled across him, asleep and protected by the Plasm Wraith.

When the group draw near the Plasm Wraith to save the Captain, the creature enter a defensive state and absorb Olimar to act as his shield, the group dispatch the protoplasm surrounding the Hocotatian and start their escape believing that the Plasm Wraith was Killed.

Escaping the Formidable Oak
Brittany goes ahead with Olimar carried by Pikmins while the two remaining Captains search for more information about what just happened only to found a note written by Olimar about the "Mysterious Life Form", the two Captain then decide to follow Brittany and the Pikmin within the Oak only to be greeted by a larger version of the "Mysterious Life Form", after supposing that it is another member of the Plasm Wraith's species, their scientific tools reveal that it is the exact same Life Form, meaning that the Plasm Wraith is "Immortal", the Capitains in panic decide to flee from the Oak while being chased by the Plasm Wraith.

Fighting the Plasm Wraith
Once the Capitains succeed in escaping the Oak with Olimar, the Plasm Wraith emerge from the inside of the Oak, take a humanoid form and absorb Olimar for a second time, forcing the group to fight the entity back.

Escaping PNF-404
Once defeated, the Plasm Wraith is confirmed to be alive and unharmed (the same way he came back after his first defeat) during the cut-scene where the S.S Drake leave the planet for good.

Trivia

 * The Plasm Wraith's Japanese name is "Amenyuudou", which can be a portmanteau of "amoeba" (written in katakana like "ameba"), an unicellular organism usually found in water, or "ame", which means "rain", and "Nyūdō" (入道) which means "priest" or "monk". Its name could also be an allusion to Wanyūdō, the guardian of the gates of Hell in Japanese mythology.
 * The Plasm Wraith is currently the first and the only boss in the Pikmin series to have a clearly-defined multiphased battle, with a "chase phase" and a "battle phase" separated by a cutscene.