The Blue Orb was under the possession of Blubi. Upon finding him, Blubi was frozen requiring Bowser to thaw him out with his fire breath. However, as Blubi is freed, he has developed amnesia. The heroes must keep talking to him in order for Blubi to regain his senses. Blubi then gives the heroes the Blue Orb.
The Red Orb was under the possession of Rebbi. Rebbi has been fighting off the Skellobits the entire time and has been worn out from battle. He asks the heroes to help assist him in defeating the rest of the Skellobits. After Mario and the others defeat the Skellobits, Rebbi gives them the Red Orb.
The Yellow Orb was in the possession of Yebbi. Due to the attack by Bonetail and the Skellobit army, Yebbi has hidden himself in a restroom refusing to come out. The only way to get Yebbi to come out is to say that they are monsters and Yebbi knows a real monster won't reveal their true identities. Yebbi then gives the heroes the Yellow Orb.