| Joining the Team Rocket | Rocket Gideon | Azalea Town | The player must show their loyalty by letting one of their Pokemon be turned into a Shadow one | Access to the Team Rocket backrooms |
| Giovanni's Private Collection | Rocket Ariana | Viridian City | Deliver a specific, rather rare Pokemon, to the Team Rocket | Access to the Team Rocket's Shadow Pokemon traders |
| The Team Rocket's Research | Rocket Tabitha | Saffron City | The player must steal the blueprints for a new kind of Pokeball | Access to the Team Rocket secret greeting, which allows to get free stuff at bars and hotels run by the Team Rocket |
| A New Pokemon Species | Rocket Viper | Mahogany Town | The player must track the DNA left by an ancient Pokemon | Access to the Enshadowing Machine |
| The Lost Experiment | Rocket Giovanni | Cinnabar Island's Pokemon Mansion | After cloning Experiment #150, the Team Rocket lost it. The player must find 3 clues of its current whereabouts | Access to the Rocket Daycare, which increases the level of Shadow Pokemon |
| The Clone in the Cerulean Cave | Rocket Giovanni | Cerulean Cave | The player must find Experiment #150. If they are in good terms with the Team Rocket, Giovanni will demand that Mewtwo is handed over after capture. Otherwise, the player will have to fight him beforehand | Access to the Giovanni's roster of Shadow Pokemon |
| The Ancestral Pokemon | Rocket Giovanni | Cerulean Cave | The player must use Mewtwo to lure out Mew, with a chance of capturing it | x1 Masterball |