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Mission mode is the Challenge Mode of Pikmin 3. In Mission mode, the player can complete one of three possible challenges, each which are 5–15 minutes long and are meant to help improve the player's Pikmin skills of gathering fruit, battling enemies, and defeating bosses.
These are the 26 stages in Mission Mode:
- Tropical Forest
- Silver Lake
- Thirsty Desert
- Twilight Hollow
- Shaded Garden
- Tropical Forest Remix (Collect Treasure only)
- Silver Lake Remix (Collect Treasure only)
- Thirsty Desert Remix (Collect Treasure only)
- Twilight Hollow Remix (Collect Treasure only)
- Shaded Garden Remix (Collect Treasure only)
- Tropical Wilds Remix (Battle Enemies only)
- Garden of Hope Remix (Battle Enemies only)
- Distant Tundra Remix (Battle Enemies only)
- Twilight River Remix (Battle Enemies only)
- Formidable Oak Remix (Battle Enemies only)
- Fortress of Festivity
- The Rustyard
- Beastly Cavern
- Forgotten Cove
- Clockwork Chasm
- Armored Mawdad (Defeat Bosses only)
- Vehemoth Phosbat (Defeat Bosses only)
- Sandbelching Meerslug (Defeat Bosses only)
- Scornet Maestro (Defeat Bosses only)
- Quaggled Mireclops (Defeat Bosses only)
- Plasm Wraith (Defeat Bosses only)
All modes in Mission mode support 2-player split-screen co-op.
The goal in Collect Treasure mode is to use the provided Pikmin to collect as many fruit and/or enemy carcasses as possible within a limited amount of time. When fruit is hauled back to the SPERO, their value will be converted to Pokos. The player's score will be based on how many total Pokos were earned and, if the player gets a platinum medal, how long it took the player to complete the area. Pikmin are found either buried, scattered across the map, hidden below plants in little groups, or inside certain enemies, like the Medusal Slurker.
When a level is complete, the player can watch a top-down playback of the entire level session, showing icons to indicate the leaders, fruits, enemies, and Pikmin.
Depending on how many Pokos you obtain, you will receive a ranking. From worst to best, they are bronze, silver, gold, and platinum. To obtain a platinum ranking, you must collect all fruit and enemy corpses on the map before time runs out. This ranking system works similarly in the Battle Enemies mode.
The objective of this mode is to defeat enemies to score points. The enemies you defeat hold a certain amount of points. For example, the Swooping Snitchbug holds up to 30 points. Once the timer is up, the points the player gains are counted as your score.
This mode requires the player to defeat a certain boss with a given assortment of Pikmin. Below is a list of all of the fightable bosses in the mode:
- Armored Mawdad
- Vehemoth Phosbat
- Sandbelching Meerslug
- Scornet Maestro
- Quaggled Mireclops
- Plasm Wraith
The player's medal is determined by the time left over. Pikmin count has nothing to do with scoring.
On the 1st of October, 2013—during that month's Nintendo Direct—Iwata announced downloadable content for Pikmin 3's Mission mode. Nintendo offered stage 5 for free if you update Pikmin 3.
On the 6th of November, 2013, a second DLC was available for purchase. This DLC consists of four remixed Story mode maps for Battle Enemies. Nintendo offered stage 5 for free if you update Pikmin 3.
On the 2nd of December, 2013, a third DLC became available for purchase. This consists of five stages for Collect Treasure and Battle Enemies and takes place on entirely new stages. Olimar and Louie are playable in stages 13–15 but Louie must be rescued before he can be used. Nintendo offered stage 11 for free for those who update Pikmin 3.
The following packs are available in the eShop:
- Round 1: "Collect Treaure" Pack (Stages 7-10) for $1.99 USD.
- Round 2: "Battle Enemies!" Pack (Stages 7-10) for $1.99 USD.
- Round 3: "Collect Treasure and Battle Enemies!" (stages 12-15) for 4.99 USD.
- Mission mode and Bingo Battle are the only modes in Pikmin in which you can find Purple and White Pikmin.
- The music that plays during all stage, with the exception of stages 11–15, was used in all of the Pikmin 3 trailers.
- Mission mode and Bingo Battle have an exclusive miniboss, the Baldy Long Legs. It appears plentifully in both modes, although it is never found in Story mode, but Story mode does give players some Arachnorb action with the Shaggy Long Legs.