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A Bonus Mission is a type of Mission which can be attempted for Generations 4, 5, and 6. In Generation ∞, any sort of mission was unnecessary to be added to that Generation, therefore Free Play was the substitute and the main game mode.
Bonus Missions are quite abundant in the Generations they appear in. There are four types of Bonus Missions in Generation 4, five types of Bonus Missions in Generation 5, and six types of Bonus Missions in Generation 6. Bonus Missions are not Part-specific; three Bonus Missions (the most ever seen in the series, SS) are all playable in Generation 6's The Black Region. All Bonus Missions to be completed, according to completion objectives, are not required to obtain 100% completion for the series as a whole.
Bonus Missions award rare items for completion, such as the True Turtle Shell (accessory), the Broken Hero Sword (impossible item to obtain in all Generations prior to 5), and the Sprinkled Chocolate Orb (attack) (one of the most sought after items in the entire series).
Eerily, Generation 6 is the only Generation which does not feature a Bonus Mission in all of its Parts, lacking in The White and Purple Regions.
The following is a list of Bonus Missions, including their location in which they take place, in chronological order and their possible rewards.
G4 and G5[]
Incomplete
G6[]
P1 and P2[]
No Bonus Missions
P3[]
S4[]
C5[]
Hourglass Purple Coin Bonus Mission[]
This Bonus Mission is located in Volcano #5 of The Fire Industry Volcano System. There are three minutes available to collect each of the 100 Purple Coins in order to unlock a glass Purple Coin Door on the floor of the third volcano. The door leads to a Gold Chest, able to reward items such as a Shadow Orb (light source), Kuribo Shoe (accessory), and at best a Power Manual +.
P5[]
S1[]
C7[]
Stopwatch Purple Coin Bonus Mission[]
This Bonus Mission is located at the very beginning of The Honeycomb for Section 1 of Part 5. There are infinite minutes available to collect each of the 100 Purple Coins located all across The Honeycomb in order to unlock a glass Purple Coin Door at the very end of The Pentagon, which is also where one of the Star Chips are located. No notice of any purple coins is visible at all if the Bonus Mission is not attempted, but when it is completed, a Purple Warp Pipe will elevate from the metal floor in the Star Chip room. The pipe leads to a secret room with a Platinum Chest, being one of the very hard missions to complete successfully, able to reward items such as a Technical Machine, a Hidden Machine, an Ice Scroll (accessory), a Spell Book for a random Magic Electric spell, and at best a Revolution Medal (accessory).