Enter Shadow (Part 1)

New Townsville: Science lab

The heroes return to the lab, and the Powerpuffs de-transform.

"Well, we got our butts handed to us." Sonic said.

"Hopefully, it will go better tomorrow." Poochi said.

"Good thing tomorrow's saturday, that means we can start searching for the Emeralds early, since we don't have to go to school." Buttercup said.

"You guys can stay here at the lab for the night, tomorrow, we resume search." Ken said to Sonic and his friends.

"Well, see ya tomorrow." Blossom said as she, Bubbles, and Buttercup left the lab.

(The next day)

Blossom, Bubbles, and Buttercup are already hanging out at the lab as Professor Utonium, and Ken attempt to track down more Chaos Emeralds.

"We'll have to use the Emeralds to increase the range of the tracker, if only we got that Blue Emerald, it would be much easier, but, at least we have two." Ken said.

"This time, we better make sure we don't run into Chaos again." Sonic said.

Then, there's a knock on the front door. "I wonder who that could be." Professor Utonium said.

"I'll get it." Bubbles said as she ran to the door.

Bubbles open the front door, but she's surprised to see no one there. "That's strange." Bubbles said, but then she found a note on the steps.

"Listen well, to whoever reads this. I know about Chaos and that you're collecting the Chaos Emeralds to keep them from him. Me and my friend can help you, come alone to the abandoned warehouse, I can't take chances that Chaos is spying on me, and leave the Chaos Emeralds behind, we don't want him getting anymore." the letter said.

Bubbles was confused about the letter, but she decided to investigate anyways.

New Townsville: Abandoned warehouse

Bubbles arrived at the abandoned warehouse and started looking around.

"Hello? Is anyone there?" Bubbles asked. "I'm looking for someone who wrote this letter."

"I'm over here." A voice said, and the owner of the voice revealed himself to be none other than Shadow the Hedgehog.

"Who are you?" Bubbles asked.

"I'm Shadow, Shadow the Hedgehog." Shadow replied.

"So she's one of these Powerpuff Girls that pretty much everyone here talks about?" A female voice asked, and it's revealed to be from Rouge.

"I'm Rouge the Bat." Rouge said as she revealed herself.

"Why did you call me here?" Bubbles asked.

"Because I need to give Sonic these." Shadow said as he revealed the Red and Green Chaos Emeralds.

"Wow, two more Chaos Emeralds." Bubbles said.

"I need you to take me to Sonic so I can..." Shadow said, but gets interrupted when something causes a rumble in the factory. "No, don't tell me..."

A puddle of water flows into the room and reshapes into Chaos, who now have the Yellow and Blue Chaos Emeralds merged into himself, have become Chaos 2, with metallic skeletons on his upper arms.

"It's Chaos!" Rouge shouted.

"But I thought he gave the Blue Emerald to Eggman." Bubbles said.

"That doesn't matter, we have to fight." Shadow replied.

"Right." Bubbles said and she transformed.

Chaos 2 attacked the three with a burst of water, which send them to the wall.

"Chaos Spear!" Shadow attacked, but Chaos 2 forms a shield to block it.

"Bubble Blaster!" Bubbles bombard Chaos 2 with bubbles, but Chaos 2 pops them all.

"Let me take a kick at him." Rouge said as she tried to attack Chaos with a kick, but Chaos 2 lets it pass through him. "Well, that didn't work."

Chaos 2 whacked Rouge with his lower left arm, and sent a wave of water at Shadow and Bubbles to send them to the wall again.

The heroes return to the lab after they failed to get the Blue Chaos Emerald. The next day, Bubbles discover a note from Shadow, and goes to the warehouse to meet him and Rouge. But unfortunately, Chaos, as Chaos 2, shows up uninvited. The three attempt to fight him, but he overpower them. To be continued...