Brain's Missions are the endgame content of Skylanders: Imaginators, discovered by the Ancient as he locates evildoers. Randomly assigned every time the M.A.P. is loaded, they range from three to five scenarios in Adventure levels, with smaller objectives.
- Scenario 1 - Lost Crypt of Ahoogah - Cali assigns the Skylander to find Blobbers in a regular dungeon layout, after he got lost looking for treasure.
- Scenario 2 - Mags' Favorite Dungeon - Mags assigns the Skylander to disarm bombs, fighting enemies in a darker version of the dungeon.
- Scenario 3 - Sharpfin assigns the Skylander to rescue plumbers in a flooded dungeon.
- Scenario 4 - Molten Lair - Buzz and Flynn assign the Skylander to locate an artifact in a lava-filled dungeon.
- Scenario 5 - Eruptor and Avril require the Skylander's help to freeze lava spots with a device similar to the one found in the Sensei Fire Realm, in a lava-filled dungeon.
- Scenario 1 - The residents of Calamity City need the Skylanders to stop the Mayor/King/Super King's rule over the town.
- Scenario 2 - Buzz needs the Skylanders to stop a pirate invasion of the town.
- Scenario 3 - Tessa asks for help from the Skylanders to rescue the citizens of a town about to be burnt to the ground.
- Scenario 1 - Jet-Vac needs help from the Skylanders to destroy an evil Creationtron.
- Scenario 2 - Buzz needs help from the Skylanders to destroy the 5 towers created by the evil bots.
- Scenario 3 - Flynn needs help from the Skylanders to destroy balloons and the Creationtron that created the balloons.
- Scenario 4 - Gumbus needs assisstance from the Skylanders to destroy walls created by the evil bots.
- Scenario 1 - The Skylanders must defend the Sky Fortress from a Vulture fleet.
- Scenario 2 - Blobbers requests the help of the Skylanders to rescue Mabu baloonists from Vultures.
The missions take place in BattleBrawl Island, adding new hazards and set enemies.
- Scenario 1 - Sal requires the Skylanders to fight in the arena so he can sing the National Anthem he created.
- Scenario 2 - Eruptor needs the Skylanders to fight after he was banned for his lava-barf attack.
- Scenario 3 - Stealth Elf needs the Skylanders to fight after she was put on trial.
- Scenario 4 -Trigger Happy needs the Skylanders to fight on Gold Giveaway Night for extra cash.
- Brain's Missions resemble the Bonus Missions from Skylanders: Swap Force, though much shorter and simpler.
- In Scenario 3 of the Dungeon missions, Sharpfin momentarily breaks the fourth wall by mentioning he met the Skylanders in an "earlier game", before correcting himself.