The game differs from previous installments, instead of treasure collecting, the captains are focusing on saving the Pikmin race which has contracted a deadly virus. The virus has been disturbing natural wildlife and surrounding planets in the atmosphere. Olimar, Louie, Alph, Brittany and Charlie have been assigned to stopping the outbreak of this virus.
During a conference call on Kopai regarding the planet's space program, a horde of Pikmin crash land on the planet. Alph, Brittany and Charlie are happy to see their old friends, but they soon learn that the Pikmin are effected by a virus called Weival's Kiss. Over on Hocotate a similar disturbance has occured from the Pikmin.
The 3 captains on Kopai are sent back to PNF-404 in the S.S. Drake to investigate along with Olimar and Louie from Hocotate in their S.S. Dolphin. Upon arrival, the two Hoctate captains crash land, and explore the terrain during the night to find the S.S. Drake. Olimar and Louie discover a nocturnal species of Pikmin, known as the Night Pikmin, which help them successfully find the S.S. Drake. The next morning, Alph, Brittany and Charlie head out into the Woods of Faith whilst Olimar and Louie begin to formulate a cure for the virus.
Alph, Brittany and Charlie find the Red Pikmin under attack from the Weival's Kiss virus. The three captains save the Pikmin and return them back to the ship, following that they begin searching for things to use to formulate a cure for the virus. That night, Olimar and Louie discover a harvest of elements for the cure are over in Orchid Willows and the next morning the captains search in this new area.
The initial search of Orchid Willows finds Yellow Pikmin, which soon lead to the discovery of the Winged Pikmin. Finally the captains find the harvest of cure elements, guarded by a Leviathan Melonrock, which they soon defeat and recover all the cure elements.
Pikmin: Evolve remains faithful to the series, including the realt-time strategy, top-down focused gameplay the series is known for. The main new feature is nighttime exploration with Olimar and Louie.
During the night, no Pikmin can be taken for exploration, instead Pikmin that have contracted the virus known as "Weival's Kiss" are to be cured using an antidote created during the day by Alph, Brittany and Charlie.
In daytime sections, the player traverses the location as Alph, Brittany and Charlie and find ingredients that can be used to create the Weival's Kiss antidote. 100 Pikmin can be taken out of their onions and used to help traverse the land and bring ingredient's back to the space ship.
Also being introduced to the series is the antidote mechanic, which plays similar to the food mechanic in Pikmin 3. The ingredients collected during the day by Alph, Birttany and Charlie formulate bottles of antidote that can save Pikmin from Weival's Kiss. Olimar and Louie use the antidote on new Pikmin that have caught the virus. One bottle can cure all controlled Pikmin at the end of each night.
Night Pikmin are dark beige in color, and are nocturnal. Due to being nocturnal, they have adapted to the challenges of night, garnering large amounts of health to put up a fight with nocturnal creatures, and being able to light up the nearby area.
They are the second Pikmin type to be found, and are discovered at the Woods of Faith. Aside from their special night powers, they are relatively ordinary Pikmin, having normal speed and normal attack power.
The game is split up into six different areas for the Captain's to explore. These sections are gradually unlocked as Pikmin are cured and the virus is being prevented.
- Woods of Faith
- Orchid Willows
- Fallen Highlands
- Disciple Coast
- Burnt Rose Wastelands
- Ground Zero