The spirits of some unfortunate Pikmin.

Pikmin Extinction occurs when every single Pikmin, including those planted in the ground and stored in the Onions, are lost. The day ends immediately afterward, due to the fact that without Pikmin, the player cannot perform any useful activity, and the Onions each produce a single seed at the beginning of the following day.

In Pikmin, the following is Olimar's Journal entry on the first day extinction occurs:

"The Pikmin have all perished because of my own carelessness. I am an utter disgrace as a leader... How can I continue to collect parts without them? Still the Onions join me in low orbit, as if this Pikmin extinction had never happened. I shan't sleep tonight..."

Olimar after Pikmin Extinction has occurred.

After extinction, the player must regrow all of their armies from one single Pikmin. If players do not treat the one to three Pikmin given to them with care, they will be easy prey to all manner of enemies and could quickly lead to another extinction. To prevent this from happening, the safest place to grow Pikmin after an extinction is The Impact Site in the first Pikmin game, and in Pikmin 2 the Awakening Wood is safe so long as one does not stray too far from the landing site.

In Pikmin 2, Extinction will occur when all Pikmin are lost in a cave, and Olimar and Louie are forced to leave the cave, most likely due to lack of protection of the Pikmin and inability to claim treasure. All collected items will be lost since this is technically leaving without using an exit geyser.

Pikmin Extinction is also a victory condition in Pikmin 2's multiplayer mode.

In Pikmin 3, Pikmin Extinction can only occur in Mission Mode and Bingo Battle. If all of one species of Pikmin die in Story Mode, the Onion will expel 1 Seed of the once-extinct Pikmin species. In Mission Mode when you lose all of your pikmin, your captain will sigh, look towards the ground, and then the spirits of all the dead pikmin rise to surround you.