Okay here's chapter 4! No one has really replied, but I love this story too much to care! Time for annoying disclaimers!
Disclaimer- I don't own any Sonic Characters except MJ. If I did own them I would be writing Sonic Manga books right now.

Chapter 4
Returning and plans with Shadow
10am. 5 days after the Ark incident.
MJ woke up and found herself tied up and locked in a prison cell. Shadow and Sonic were in the same cell but she couldn't wake them up until she untied herself.She used an Ice blast to freeze the ropes on her back and destroyed the ropes by slamming herself onto the floor which made the ropes and ice shatter. She proceeded to help Shadow and Sonic who were still knocked out from the gas. She untied Shadow first who was beginning to wake up along with Sonic who broke free on his own.
"So how do we get out?" MJ asked.
"Hmm knowing Egghead he probably put us underwater or something so I couldn't stop him." Sonic informed.
"I can see water above the cell roof but I don't think we can break these bars." Shadow said while attacking the bars with a homing attack.
"I could try to freeze them with Ice and you 2 could attack the bars...but then how could we escape. Sonic can't stand water and I don't think I can hold 2 people at once." MJ explained.
"You could take us one at a time." Sonic suggested.
"Let's go with her plan. MJ shoot an ice blast at the bars and take us through the water one at a time." Shadow commanded.
"Shadow, you could always use Chaos Control to teleport us outside the base." MJ said just remembering his special trick.
"Okay time for a little Chaos Control!" Sonic cheered.
Shadow used Chaos Control and got them out of the base, but guard robots saw them and began to chase them. Sonic easily destroyed them with a homing attack and they ran off to the Thorndyke mansion.

Meanwhile at the Thorndyke residence

Amy was in a huge rage. She hit a stuff animal with her hammer making the stuffing come out and her just get madder and madder.
"WHY HASN'T SONIC COME BACK YET?" Amy screamed once again nearly making Knuckles' ears bleed.
"You know how Sonic is Amy. He likes to run off instead of sitting in one spot." Tails told her. His ears ringing from Amy's latest scream.
The front door bell rang and Amy ran down the steps faster than Sonic running from Eggman. She opened the door and found Sonic standing there with MJ and Shadow next to him.
" SONIC! YOU'RE BACK!" Amy cheered and tried to hug him but he ran to the kitchen to get some food.
"Who's she?" Shadow asked.
"She's Amy. She helped you remember a promise you made to Maria." MJ told him.
"Did Shadow loose his memory or something?" Amy asked.
"Yeah but he's remembering stuff." MJ told her.
Shadow remembered something. It was Maria's promise.
Flashback
Shadow and Maria were running down a hallway she got shot at but kept running and put Shadow in an escape pod.
"Shadow... I beg of you... please, do it for me... for a better
future-" Maria said.
"Maria!" Shadow cried.
"For all the people who live on that planet...give them a chance to be happy. Let them live for their dreams. Shadow I know you can do it. That's the reason you were brought into this world. Sayonara, Shadow the Hedgehog." After Maria said her plead she ejected Shadow from the colony and died.

End flashback

"Maria..." Shadow quietly said to himself.
"Shadow you coming?" MJ asked as she started walking to the kitchen.
"I'll be back later. I need to clear my head." Shadow told her just before running out the door.
MJ signed. She at least hoped that Shadow would eat some breakfast with her. She went to the kitchen and started eating with Sonic, who was eating like a starved prisoner would.

Meanwhile

Shadow was running through the streets of Station Square trying to see if anything else would trigger his memory. He went past the bank and remembered him stealing the Chaos Emerald for Eggman, but that was all he remembered.

Meanwhile

Sonic had just ran out the door away from Amy who was trying to hug him again. Amy pouted and walked over to MJ.
"So, do you think he'll like you too someday?" Amy asked while smiling at MJ who had just spewed out her water she was drinking due to Amy's question.
"What are you nuts! He doesn't even remember me or really anything yet." MJ told her as she began to clean up the mess she made.
"Oh I was just wondering! Besides we all know you like him. Maybe after he gets more of his memory back...he'll start asking you out..."
"Please Amy. He'd never do that. I know because he didn't like me on the Ark so why would he like me now!"
"Well. If you're kind to him and help him get his memories back...he might just ask you..."
"Please. That'd only happen in my dreams." MJ said. She covered her mouth after realizing what she just said which made Amy smile.
"You know what they say...Wishes are eternal."
"Yeah. Sonic'll probably ask you out someday when he actually starts to like you." As soon as MJ said that Amy hit her with her hammer.

Meanwhile

Shadow continued thinking not about his past, but about the people he met.
"That girl...MJ I think she's called. Has helped me more than anyone else I can remember..." he thought.
"Could I...possibly have feelings toward that girl?" He asked.

Later

MJ was sitting on the couch waiting for Shadow to return. He hasn't been back to the house since he left earlier and now MJ started to wonder if he ran away.
"I knew it. He ran away from us." MJ said to herself.
Tails came back from the workshop covered in oil and grease. He got some paper towels from the kitchen and began to clean himself off.
"Last time I do that again..." Tails mumbled to himself.
"Hey Tails. Working on the X Tornado again?" MJ asked.
"Yeah but I made a mistake and got oil and grease all over me."
"Here I'll help" As MJ said that she got some more paper towels and helped clean up Tails. She was still worried about Shadow, but she needed to take her mind off of him.
"Thanks. What are you doing in the living room anyway?" Tails asked.
"Nothing really just flipping through cannels and stuff." MJ lied to him.
"Shadow still hasn't come back yet?"
"No. I think he ran away. He must not be used to remembering everything yet."
"Maybe or Eggman might've found him again."
MJ considered that thought for a few minutes, but Shadow came in soon after and sat on the couch.
"Where have you been?" MJ asked Shadow who was lying on the couch staring at the ceiling.
"Nothing that I need to tell you." Shadow replied bored.

"Oh okay sorry."
"It's okay."
"...Um would you like to hang out tomorrow or something? I could show you places you've been before..."
"Okay."
MJ smiled. She never thought she'd be able to spend time with Shadow, especially alone. She couldn't wait for tomorrow, but she had to stay cool in front of Shadow.
But, a certain somebody heard the conversation. It was none other than the love sick hedgehog herself, Amy. She would've squealed with happiness, but she didn't want the two to hear her.

There's chapter 4! The next chapter will have romance, even if it's not much. Please keep replying!