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When Luigi first enters the Trainer's Room, the key is placed in a cage. The purple Spirit Balls appear and turn it into a golden rabbit. Luigi or Gooigi must grab the rabbit with the Poltergust G-00 while the other uses the Dark-Light Device to turn it back into a key. The blue gem can be found inside the piggy bank at the upper-left corner of the room.
After Nikki, Lindsey, & Ginny scrambled the door ways, the Trainer's Bedroom will not be visited until Luigi captures the magicians.