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Elm tore through his lab. He furious that someone had dared take Pokemon from his own home. After searching everywhere he came back the main room where Officer Jenny was questioning the witnesses.

Jenny: "So let me get this straight, you don't have ANY kind of security here at the lab?"
Elm: "Ive never needed any until now... I use to have a Charmeleon at the front but it got bored and ran off..."
Jenny: "Well then its your own fault but rest assured we will get to the bottom of this."
Growlithe: "Groo! Grrrrrroooollllll....." Officer Jenny's Pokemon began digging at the bottom of the glass case where the balls were being held. After further investigation a hole was discovered.
Jenny: "Well well well! Lets find out where this leads to.
Everyone hopped into the hole and began walking along a poorly dug tunnel.

Marty: "I can't imagine who could dig such an odd hole and then not even bother making a decent road!"
Alexander: "Marty, they were too busy stealing our Pokémon."
"I know that its just...they dont know who they're messing with!"
Riley had to admit. In Johto, stealing another trainers Pokemon was...basically forbidden! But no one really thought about it much because, what kind of horrible, awful cruel person would steal a Pokémon??

Meanwhile in that same clearing..........

James: "Jesse, Im hungry!"
Jesse: "Well you're just going to have to deal with it."
Meowth: "The real thing we have to deal with is this Totodile that keeps tryna pop outta its Pokeball!"
Jesse: "Just keep it in the bag with the other pokeballs. Once we get it to Giovani, he will know what to do with it.
James: "Im not sure we can keep it contained for too much longer...
Jesse: "We just need to wait a little longer..."

When the kids reached the end of the tunnel they saw three figures standing near a hot air ballon trying to hold onto a big brown bag going crazy!

Totodile: "Grrroww!!!!!!!"

Professor Elm: "That sounds like Totodile!"
Jenny: "Alright team Lets get ready to move in!"

The trio spotted the kids and jumped into the air balloon. Meowth couldnt hang onto the bag any longer and dropped it after they took off.
Jesse/James: "MEOWTH!"
The bag dropped and Totodile sprung out and landed in front of the team and started dancing in circles.

Riley: "Looks like you've got your work cut out for you."
Marty: "Hey he saved all of our Pokémon!"
The hot air balloon rose up and started drifting away quickly.
Jesse: "Ohh no you don't! Growlithe, flamethrower!"
A stream of fire shot out at the balloon and it was sent flyying into the distance!

Team Rocket: "It looks like team rocket is blasting off agaain!"

Totodile jumped up and down happily and then ran over to the bag where the other pokeballs were waiting. After getting the flame designed ball Riley looked over and watched Alexander meeting Chikorita for the first time and she thought about how happy she was feeling to finally meet her new partner.
Riley: "Cyndaquil! I choose you!"
Everyone stood there in silence. Riley could only gasp.
Cyndaquil's were normally just bigger than a football. This Cyndaquil was just bigger than a pickle jar!

Marty: "Looks like YOU have your work cut out for you as well.."
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Chapter 3:
-Riley runs into a legend on her way to Cherrygrove city.