- Pokemon Mystery Dungeon RPG: The Gates of Time
- Pokemon Mystery Dungeon RPG: And so, it Began
- Pokemon Mystery Dungeon RPG: The Fabrics of Space
- The first game made was The Gates of Time. However, And so, it Began was made to explain how Cyndaquil, Squirtle, and Chikorita became a rescue team (now known as the Cool Pals) as seen in Gates of Time.
- There is an entirely new team in The Fabrics of Space.
- Even though the first game's team was the first playable team, Team Cool Pals is the most prominent, due to them being present in along two games instead of one and also their own TV series (not present in their world).
- The Pikachu that leads the third team actually has a trainer.
- Miltank, Mt. Moon Peak (1 and 2) Planet Moomoo's Moon (3)
- Cacturne, Hippowdon Desert (1)
- Cacnea, Hippowdon Desert (2)
- Primal Rayquaza, Hidden Oasis (1)
- Primal Kyogre, Hidden Oasis (2)
- Abomasnow, Mt. Ice Peak (1 and 2)
- Muk, Toxic Mine (1)
- Grimer, Toxic Mine (2)
- Raichu, Mt. Thunder Peak (1 and 2)
- Primal Dialga, Time Coliseum (1)
- Primal Mew, Cave of Secrets (2)
- Electrode, Planet Blowsit's Moon (3)
- Marshtomp, Planet Aquaris's Moon (3)
- Dusknoir, Planet Creepyspook's Moon (3)
- Garbodor, Planet YuckYuck's Moon (3)
- Dragonair, Planet Swiftzero's Moon (3)
- Magmortar, Planet Burnscorch's Moon (3)
- Primal Palkia, Planet Earth's Moon (3)
- Gengar, Sinister Woods (1,2), Frosty Prison (3) (Can be fought in all games) (Optional)
BTW, 1 stands for Gates of Time, 2 is And so it Began, and 3 means Fabrics of Space