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YoshiEgg and Bloop had just defeated Overman Supreme and were relaxing back home. When suddenly, a loud boom is heard and Bloop is knocked out. When he awakens, YoshiEgg is gone and Bloop is alone. "Bloop, it's your time" spoke a voice near him. Bloop held up one of his tentacles. On it was a small wristwatch. "Hm?" asked Bloop, confused. "YoshiEgg has been taken away by Overman Supreme's goons. You could save him later, but that's not your top priority." "I don't get it...." said Bloop. "Your not supposed to. You will be a secret agent." "Why?" "Because of unknown reasons. My name is Voko, and I will be your guide." "So do I get to save YoshiEgg?" "Not yet. First you have to go on some missions." "Again, why?" "Because YoshiEgg's disappearance may not be considered a threat yet. You'll learn about why he's gone in time." "Do you know? You act like you do." "No. But Overman Supreme and friends are responsible for many evil happenings, so you may run into them on your adventures." "OK" concluded Bloop, who set off to learn about YoshiEgg's dissappearance and save the world.
For more, see Secret Agent Bloop/story.
- Agent Bloop - The main character, Bloop is the player for most of the missions. He can run around, jump, and be very stealthy. He has a variety of tools to sneakily sneak around and save YoshiEgg.
- YoshiEgg Nook - You play as him at certain breaks in the story. His tools are more weapons then stealthy abilities, and he takes on many monsters as he tries to escape.
- Voko Hologram - You play as a hologram the mysterious Voko made when fighting some bosses that Agent Bloop is too weak for.
- Helga Blooper - A Blooper Nanny who accompanies Bloop on his adventures, Helga can command some baby bloopers to do things for Bloop to help him get into special places.
- Voko - A mysterios unseen person who helps Bloop by giving him advice.
- Lady Cheep - A rich cheep-cheep, the daughter of Dr. Maw.
- Dr. Maw - A strong, rich business man. The name may suggest relation to Dr. Claw, but it is not confirmed.