Here's chapter 3! Thanks for replying!
Disclaimer- I don't own Sonic or any Sonic people. I only own MJ. If I did own them then pink bunnies would have taken over Japan.

"You should know where the first one is." Eggman said. Sitting in a chair next to a giant computer.
"Well I don't so just tell me."
"The first Emerald is in the Thorndyke mansion, where you just happen to be staying."
"I never knew they had one" MJ thought. "Okay I'll be back."
MJ started to walk out of the lab.
"But...if you do anything, and I mean ANYTHING to Shadow I'm not going to help you anymore." As MJ said that she left to get the first Chaos Emerald.
"I'm not going to do anything...much." Eggman cackled. He began typing on his computer. Finding the next coordinates of a Chaos Emerald.

By the time MJ got back it was morning. She knew she wouldn't be able to get the Emerald now. Tails would probably be working on it to use with the X Tornado. She walked into the house to find nobody was awake, and she crept to her room. Until, she bumped into Amy of course.
"So...you love Shadow huh?" Amy said with an evil smile on her face.
"W-what! What would give you that idea!" MJ questioned confused.
"Well for one, you cried your heart out on the Ark, and two I persuaded Cream to tell me what you said.
"You and everyone else in the world knows that..." MJ mumbled.
"What was that?"
"Uh nothing..."
"Well want to help me make breakfast? You could get some cooking lessons in case Shadow's alive."
"Okay..."and as MJ said that she followed Amy to the kitchen and helped her to cook.

Meanwhile

Sonic was beginning to wake up on the roof. He could smell breakfast from the kitchen and jumped in to see what was cooking. Amy and MJ had make pancakes and waffles. Amy made her with blueberries to give them the color of her favorite blue Hedgehog, while MJ just make plain pancakes.
"Dig in!" Amy shouted cheerfully. Everyone began to eat except MJ who didn't feel like eating. She had other more important things to think about right now.
"I can't believe I have to work for Eggman to get Shadow back...maybe I can rescue Shadow and just run away from the base in time! No...that won't work...Eggman probably already has plans incase that happens. Like erasing Shadow's memory or something..." MJ thought, but little did she know that Shadow already had something wrong with him. MJ snapped back into reality when something poked her. It was Tails.
"C'mon MJ at least eat something. If you don't you'll starve!" Tails said and everyone at the table agreed. So MJ began eating, but she didn't eat much. All she had was half a pancake before she went back to the guest house.

10pm. 4 days after the Ark incident.

MJ was about to grab the Chaos Emerald, she remembered what Rouge taught her about stealing jewels when she first met her a few years ago. MJ grabbed it and ran off to Eggman's base undetected or so she thought. Sonic had been sitting on the roof again when he saw MJ escape. He finally decided to follow her and see where she had been going.

MJ finally arrived at the base, completely regretting that she stole the Chaos Emerald. She was let inside as Sonic followed in the shadows.
"I see you brought the Emerald." Eggman announced over the speaker. "I'm going to give you so time with Shadow while I work on finding the next Emerald. Don't even think about taking him for I have guard robots who will hunt you down!" And with that Eggman released a metal hand and took the sacred jewel from MJ's grasp.
"So this is where she went last night!" Sonic thought. "I can't believe she took the Emerald. Man she really likes Shadow to do that."
MJ, Sonic and Shadow were standing in the room. MJ immediately ran over to Shadow.
"Shadow! I'm so glad you're okay!" MJ said while hugging him.
Shadow pulled away. "Who are you?" He asked.
"Shadow, it's me MJ! Don't you remember the Ark incident?"
"What's the Ark? Tell me what happened!" Shadow demanded.

MJ was shocked; she couldn't believe Shadow had forgotten everything.
"Could Eggman have done this to him?" MJ thought. Eggman probably did this to motivate her into finding the rest of the Emeralds quickly.
"I said tell me what happened, and how do you know me?" Shadow demanded yet again.
"Well you see you and me met each other when you saved my life in a cave in. Then my friends and I had to stop you and Dr. Eggman from destroying the world with the Eclipse Cannon located on the Space Colony Ark. We stopped you 2, but the Biolizard had awoken and the Colony was on a crash course to earth. You helped me and my friends stop it...but you fell from space and we thought you were dead." MJ explained.

Shadow's eyes went very wide almost as if he remembered something. He did remember something, about a girl being shot on a space colony. While he was sent in some sort of pod to another planet.

"Shadow? Are you okay?" MJ said, thus snapping him back into reality.
"Yeah I'm fine. Do you know someone with the name Maria?"
"Maria? She was your friend on the Ark...You told me yourself before you crashed to earth that is..."
"So that's who she is..." He mumbled.
"Whoa this is crazy. I better tell everyone else." Sonic thought. Until Shadow saw him...
"Hey who's that guy?" Shadow asked.
"Huh?" MJ said while looking and hers eyes found Sonic hiding behind some plant.
"Why did you follow me?" MJ shouted. Furious that Sonic was snooping.
"I saw you run away with the Emerald and decided to follow you. Then I saw Shadow and Egghead which made everything clear."
Shadow had another flashback. It showed him and Sonic having a battle and Shadow calling Sonic "Faker".
"Faker? Is he a copy of me?" Shadow asked.
"So I see you remembered something!" Sonic said cheerfully as he slapped Shadow on the back.
"No Shadow. Sonic's more of your rival. You always called him faker because you thought he was a copy of you. Until he helped you and everyone else stop the colony." MJ explained.
"Oh I see..."Shadow said very confused at all this new information he was learning about his past. Eggman walked in and was about to say where the next Emerald was when he saw Sonic.
"What's that annoying pest of a Hedgehog doing here? GUARDS ELIMINATE HIM!" Eggman ordered. A swat team of robots appeared and got confused on which hedgehog to attack, so they attack both of them.
"Get off of me you filthy machines!" Shadow shouted before finally kicking and punching them off him.
"It's time to party!" Sonic exclaimed while punching some more robots off him.

They were surrounded by robots. But, they had ways of dealing with them.
MJ froze the robots with her icy blasts, while Sonic and Shadow spin dashed through them. Then a huge robot came up behind them and grabbed the 3 heroes in its grip. The tried to escape but the hold from the robot was too strong. The robot got 2 guns out. It sprayed sleeping gas which knocked the team out instantly.

8am 5 days after the Ark incident

"SONIC! WHERE ARE YOU?" Amy shouted at the top of her lungs, thus shaking the whole house.
"MJ isn't in her room either." Chris said covering his ears.
"Wonder where they could be?" Cream asked no one in particular.
"I BET SONIC WENT ON A ROMANTIC EVENING WITH HER! SHE'S GONNA GET IT!" Amy shouted furiously.
"Yeah right. Like MJ would do that. She probably went looking for Shadow, and Sonic's out on his run." Knuckles said.
"But Sonic wouldn't be able to miss breakfast on purpose!" Amy cried.
"I'm sure he'll smell breakfast as soon as it gets on the table and come running back." Ella said in a calm voice.
"Chao chao chao?" Cheese asked. Cream being able to understand her Chao, translated what he asked.
"Cheese said well, what about MJ..." Cream explained.
" She'll probably be out all day looking for Shadow" Knuckles joked. This made Amy and Cream start attacking him.
"DON'T BE SO CRUEL!" Amy shouted one last time after hitting him hard on the head with her Piko Piko Hammer.

Yay end of chapter 3! Please reply!