The Space Colony ARK was the most advanced research centre in the history of mankind. It was first-ever Bernal sphere space colony, and was the pride of the United Federations' growing prosperity. Headed by Professor Gerald Robotnik, dubbed the most intelligent man in the world, it was used to research new medical techniques to treat incurable illnesses. In particular, the terrifying disease Neuro-Immune Deficiency Syndrome, or NIDS, was the biggest focus of the colony.

The disease was caused a genetic birth-defect, and would usually start to manifest in late-teens. It became severe in the mid-twenties, and sufferers could either die before they hit thirty, or live to reach as high as seventy with the right treatment, but there was no real cure.

Thus, Gerald's research team worked around the clock, living on the colony with many of their patients. Abraham Tower, or 'Abe' as he was known, was not one of those patients. Instead, he was only there because his parents were part of that research team. At eight-years of age, Abe could not be left to live on his own while his parents live in the ARK, and as there was nobody to look after him, he lived up on the colony with his parents.

He was the only member of the crew who wasn't a researcher or a patient, and if it weren't for Maria, he would be the only child on-board. Maria Robotnik, Gerald's granddaughter, was also a patient, whose symptoms had started to show much earlier than they typically would. She was only twelve, yet she was so mature for her age that Abe at first thought she was much older. She was the only friend he had on the ARK, and was the only reason he hadn't gone crazy yet.

"And that's how you solve this type of problem," Maria finished. While she was fun to play with, she would also regularly help Abe with his schoolwork, showing him how to solve problems he didn't understand or checking his homework for him. Not that it really mattered, though. His parents simply gave him some textbooks and a schedule to follow. He had no official teacher, and he wasn't graded on any of his work.

"Wow, thanks!" he said, and worked out the next problem on his own. "Is this it?"

"Let me see… Yep, that looks right!" Maria patted the boy's head, causing him to flinch and bat her hand away. She laughed as he protested.

"Hey, cut it out!"

The door to the room opened, and Gerald Robotnik walked in. "Maria, sorry to bother you. I'll be needing your assistance later for erm, you-know-what."

Maria nodded. "Sure, Grandfather. I'll be down as soon as I've finished helping Abe with his homework." Abe didn't know what 'you-know-what' meant. He only knew that, of all the patient on the ARK, Maria was the only one with access to the restricted areas, and was involved in some sort of project that even some of the doctors didn't know anything about. He asked her about it once, but she only said that she couldn't tell him anything. 'Confidential', she called it, whatever that meant.

Gerald regarded the boy. "I trust you are keeping well to your studies?" Abe nodded, keeping his eyes averted and not saying a word. Gerald always made him nervous. "Good lad! Your parents are some of the finest minds I know. Keep it up and you may well be like them someday."

Abe huffed, though Gerald didn't notice as he was already leaving the room. "I don't want to be like them," he muttered, now frowning as she looked down at his homework. He was suddenly far less eager to finish it.

Maria sighed. She reached out and pulled the boy into a hug. He failed his arms and tried to pull away. "I know you wish your parents would be around more, but what they're doing is important."

Abe stopped struggling. "Yeah but, the only times we ever talk is in the morning, and all they say is 'have a good day'. I don't even see them before I go to bed anymore."

"I'm sure they want to talk to you, too," she assured him. "But they also want to hurry and rid the world of this condition that makes people suffer. That way, even more families will be able to spend lots more time together. And then, they'll be able to give you their full attention."

"You think?"

Maria nodded. "When the cure is finally found, you'll be able to make up for all the lost time together. So until then, be strong for them, and show them that you're just fine. That way, they can work without regrets, and finish their research faster."

Abe smiled. "Yeah, I can do that! I'm a boy, so I can be strong! Plus, I got you!"

"That's the spirit!" Maria giggled. "Now, is there anything else you're having trouble following?"

Abe glanced over his homework. He understood the rest of it, but he knew that if he told her that, she would be off to help Gerald with whatever it was he was working on. "Uh, this stuff here…"

He pointed to a random problem that he easily could have solved. Maria looked at it and picked up her own pen and paper. "Okay, so for this one…"

As Abe walked through the ARK's hallways, wearing earbuds that played the latest popular music from the Earth, he peered into the rooms he passed by, where doctors and patients were performing their regular check-ups. Nothing serious, simply asking them questions about how they were feeling, and if there was anything that could be done to improve their lives on the ARK.

Through one door though, Abe saw two researchers that he recognised as friends of his parents'. They were on Gerald's special team, the one that usually stayed in the restricted areas, and they didn't seem to be with any patients. Curious, Abe removed his earbuds and crept towards the door.

"Shadow's really coming along, isn't he?" one of the researchers said. "To think we all laughed at the idea, and now…"

"It won't be long now until he wakes up. What if he's violent like the last one?"

"The Professor seems to have something up his sleeve, involving that granddaughter of his."

"Maria? I know he dotes on her, but isn't he letting her get a bit too close? She knows more than even us researchers."

"I know what you mean. And hey, have you heard those rumours about a mysterious visitor helping the Professor? What's that about?"

Abe wasn't sure what he was hearing; they were talking so fast and using a lot of words he didn't fully understand. What he did understand though was that it seemed to be related to whatever Gerald and Maria were working on.

"Hey!" a third voice shouted, making Abe jump. The door slammed shut suddenly, and the voices inside became muffled. "What are you doing, talking about sensitive information here?!"

"Sorry!"

"Get back to the lab. Your break's over!"

Abe listened a little longer, but the voices were gone now. Shrugging, he put his earbuds back in and continued to walk.

Abe ran through the ARK, laughing as he rounded a corner and stood against the wall. He peered around and saw Maria chasing after him. "I see you, Abe!" she said, and he bolt down the corridor. "Get back here, you scamp!"

Abe peered behind and stopped to taunt Maria, blowing a raspberry and smacking his backside. "You're too slow, Sis!"

Maria caught the boy and held him in a headlock. "Gotcha!" she laughed. He managed to wriggle his way out and continued running. "Hey!"

"Try again!" he sang, rounding another corner and crashing into somebody, falling to the floor. "Owww…" As he rubbed his head, Abe looked up to find one of the patients, an elderly woman, also on the floor. "S-Sorry, Miss…"

"Ohhhh, my hips…"

Maria gasped, rushing to help the lady to her feet. Abe also offered a hand. "I'm so sorry, ma'am. You're not hurt, are you?" Maria turned to Abe, giving him a stern look. "Abe, you need to watch where you're going."

"I'm sorry," Abe repeated, now flustered as he averted his eyes from Maria's. She was usually calm, and sweet, but that didn't mean she couldn't get angry. And when Maria got angry, she got angry.

The old lady began to laugh. "Now, now, it's all fine. It was partially my fault. I was on my way to the Bingo Night and I started rushing so I wouldn't be late. Were you two playing a little game?"

Abe nodded. "Well, sorta. There's not much to do up here."

"Not much fun with all us old folks, eh?" the lady asked, laughing again. "It's nice to see youngsters so full of life. I can no longer keep up with such high-energy games. If ya ever get tired of running, you're more than welcome to come and join us in the lounge."

"That could be fun," Maria said, turning to Abe. He didn't seem to agree.

"But, Bingo's for old people," Abe protested. "What's fun about ticking off numbers?"

"Oh-hohohohoho!" The lady wiped a tear from her eye. "You remind me of my grandchildren! Well, I'd best be on my way. Oh." She reached into her purse and pulled out a couple of sweets, offering one to Abe and one to Maria. "Here you go. Have fun, and try to be more careful around those corners."

"I will, and thanks!" Abe said, waving goodbye as the old lady walked away.

"Are you sure you're feeling alright?" Maria called out. The lady simply waved back to them as she laughed again. Smiling, Maria said, "I guess she's fine. I'm glad. But, maybe we should play somewhere less obstructive."

"Like where?" Abe asked. "This place is boring. It doesn't have anywhere fun to play."

"Well, it is a research centre," Maria said with a shrug. "Maybe I can ask Grandfather if there's a room we can set up to play games in. Until then…" Maria reached out, grabbing Abe while his guard was down. "Gotcha!"

"Wah?! No fair! I didn't know we were still playing!" Abe tried to struggle free, but she wasn't having it this time.

"Too bad! This time, it's my win." She let him go and checked one of the nearby clocks. "How about we go back now and do some reading? Can't crash into somebody in a book."

"Hey Maria, what's 'mysterious'?"

Maria tilted her head at the sudden question. "Huh?"

"Like, what does it mean?"

"Hmmm… I guess it means, something you don't know much of anything about? Like, how do magnets work? It's mysterious. Or who swiped extra dessert from the kitchen last week?" She emphasised that last question with a knowing grin. "A mystery."

Abe whistled innocently and turned around. "Dunno what you mean."

"Suuuuuure," Maria teased, roughing up Abe's hair. Abe pushed away, laughing as he straightened it out. "So, why do you ask?

"Well, I heard one of the researchers says there was a 'mysterious visitor'. What was she talking about?" Abe noticed that Maria was simply staring at him, and hadn't said anything for a few seconds. "Maria?"

"Huh? Oh." Maria held one of her hands with the other and darted her eyes around. "W-Well, I'm not sure. We get a lot of visitors, usually from the government, to check on Grandfather's progress. Maybe it was one of them?"

Abe saw that Maria was acting funny. She was fidgeting, and suddenly seemed very uncomfortable. "Are you okay?"

"I-I'm fine," she said, putting her usual smile back on. "Um, actually, I think I'm a little hungry. How about we go back and get something to eat?"

Abe watched as she walked past him, now concerned. "Are you sure?"

"Yes, I'm sure," she insisted, taking the boy's hand. "Come on, let's go back. I wonder what they're serving today."

Abe still wasn't convinced, but he could tell she wasn't going to tell him anything, so he decided to drop it.

One day, Abe's curiosity got the better of him, and he decided to explore the ARK whilst Maria was with the doctors getting a check-up. When the GUN soldiers on-duty were distracted, Abe crept by them, using his smaller size to sneak by unnoticed, and entered the restricted areas of the ARK.

He ventured through the forbidden hallways, which seemed bigger and more vacant than the ones he was used to, until he stumbled upon a room surrounded by glass. Inside that room he could see Professor Gerald, and somebody else. The other person wasn't human, though. Or at least, it didn't appear to be. It was a large, black creature with three eyes and no mouth, horns where its ears should have been, and to top it all off, it was floating!

The two seemed to be talking, and then they moved over to a console and watched something on a monitor. Abe walked closed, peering into the room through a window on the door. There, he saw a pod, and there appeared to be something inside of it, but he couldn't tell what.

Suddenly, the pod began to move. It raised up, and Abe could see the thing inside clearly. It looked like a hedgehog with black fur, and red stripes, suspended in a green fluid substance. It opened its eyes, startling the boy and causing him to jump back with a fright.

Turning around, Abe was about to run, but he stopped when he found Maria standing in his path. She had been shot in the chest, and her body was covered in blood. "Abe…" she said, staring at the boy. "Abe, run."

"Maria!" Abe ran as fast as he could, but for some reason, he wasn't making any progress. A gunshot rang out, and Maria fell to the floor. Suddenly, was in his arms, bleeding out as the last of her life faded from her eyes. "MARIAAAAAAA!"

Turning back towards the room, Abe now found himself standing in a large, pitch-black area. Bodies lay scattered before him, draped in white lab coats that were stained in blood. Among them were his parents, and standing above them all, was Professor Gerald Robotnik, grinning menacingly. The black hedgehog walked out from behind the professor, a blood-stained pistol in his hands.

"All you ungrateful humans, who took everything away from me, will feel my loss and despair!"

"NO!" Abe shouted, falling back as the hedgehog pointed its gun at him. "STOP IT!"

"ALL YOU UNGRATEFUL HUMANS, WHO TOOK EVERYTHING AWAY FROM ME, WILL FEEL MY LOSS AND DESPAIR!"

"STOOOOOOP!" Abe held his head in his hands, tears streaming down his face.

"Abe," Maria's voice echoed inside his head.

"Son," his father's voice called out.

"Abe," his mother's voice said.

"Commander," the hedgehog said as he pulled the trigger."

"Commander. Commander!"

Abraham Tower woke up, looking around to find himself inside his shuttle. He took a moment to calm down, wiping the sweat from his brow as he remembered where he was, and what he was doing. So it was all just a nightmare… A nightmare of that day, fifty years ago…

"Commander, we have located a landing position! ETA: five minutes!"

Tower looked over to the soldier reporting to him. "How long was I asleep?"

"About twenty minutes, sir!"

"That long?"

"The ARK's structural stability has been compromised, and with al; the fighting, we've had to keep our distance while we looked for a suitable place to land."

The Commander grumbled. "Why didn't you wake me sooner?"

"Apologies, sir, it's just… you haven't slept at all since this all began, right? We thought you could use the chance to-"

"I'm not sleeping a wink until this is all over!" the Commander shouted. "When Shadow and the Black Creatures are dead, that's when I can finally rest! Until then, I'll stay awake, and see this whole thing through!"

"Y-Yes, sir! Um, about that, Shadow appears to be racing Sonic the Hedgehog along the crumbling ARK."

"So we know where he is, then. Music to my ears." The Commander stood, and began to undress. "It's been a long time since I've been on the field, but I still remember how to fight. Shadow, I'll be the one to finish you off."

"Diablon is prepped and ready for launch!"

The Commander hung up his formal attire and took out a slim, black combat suit from a nearby wardrobe, designed for elite soldiers that allowed greater mobility at the cost of some protection. It was also made of a shock-absorbent material that would offer greater protection inside of the experimental mech, Diablon. Grabbing a shotgun, a sidearm, and three grenades, the Commander moved to the back of the shuttle, where Diablon awaited.

As Shadow grabbed the Chaos Emerald, he closed his eyes, a familiar feeling washing over him. "Sonic, now I remember. That day, we fought here aboard the ARK."

Sonic skidded to a halt before Shadow. "Well, looks like you won this one. That makes it one-to-one."

Shadow put the Chaos Emerald away. "I seem to recall defeating you in our last encounter."

Sonic scoffed. "Please. Your memory really is all jumbled up. I totally won that time."

"Sonic!"

Sonic pressed his earpiece. "Yo, Tails, looks like Shadow's got this one. As long as Eggman or the Black Creatures don't have it!"

"… Sonic, you realise that, depending on what my memories reveal, we might end up being enemies." Shadow entered a combative stance as he waited for Sonic's answer.

However, Sonic simply shrugged. "We'll cross that bridge when we come to it. Although, I get the feeling that, no matter what happens, you'll do the right thing. You always have done so far, at least."

Shadow didn't say anything. He simply eased his stance and chuckled under his breath. "I'm still sensing an Emerald here on the ARK."

Sonic gave a dismissive wave. "That'd be Eggman's. I saw him approaching earlier. You go do what you gotta. Tails and I are goin' over to the Black Comet to finish this off."

Shadow nodded. "Well then, we'll meet up later. And when we do, you'd best be ready for whatever happens."

Tails pulled up next to the two in the shuttle borrowed from GUN. Sonic jumped aboard, waving Shadow goodbye as they took off. Getting inside, Sonic sighed. "Man, he's really letting this get to him."

"I thought he'd already come to terms with it before," Rouge said, "But I guess it still bothers him. All this time with no clue who he is…"

"Shouldn't you just tell him?" Knuckles asked.

"I've already told him what I know," Rouge answered. "He's Shadow the Hedgehog, created fifty years ago. He tried to destroy the world, but then in the end, he saved it. And that's all I can tell him. Information on Project: Shadow is limited, and at the moment, anything more would just be speculation. Educated guesses at best."

"It must be sad, being all alone in the world without knowing your place," Amy said, gazing out the window to where Shadow was moments ago.

"He's not alone," Sonic told her. "This is just something he needs to do right now. He needs closure, even if it comes from that creep, Black Doom."

"You met him in Westopolis, didn't you?" Knuckles asked. "So, how about it? You think there's any connection between him and Shadow?"

"I'd be lying if I said I couldn't feel anything," Sonic admitted, scratching his ear. "But that feeling is where the similarities end. Even at his worst, Shadow was never a monster who preyed on the weak. He even helped Rouge out at Prison Island, remember?"

"How could I forget?" Rouge said with a wide smile. "Wasn't exactly what I'd call a gentleman, though."

"Guys, head's up," Tails said. "We've got company."

Knuckles cracked his fists and Amy pulled out her hammer as they all turned to find a swarm of Black Creatures flying towards them. "Alright," Sonic said, "Let's do it to it!"

Shadow grunted as he came back to reality, holding his head he tired to process what he had just seen. His journey through the ARK had brought him to this familiar-looking room, and upon entering, images began to flash through his head. Images of that girl, Maria, and himself. Together, they ran through the ARK, battling the Artificial Chaos alongside GUN soldiers. Professor Gerald was there, too.

The vision he had been shown earlier showed him that humanity was his enemy, that GUN had mercilessly killed the people of the ARK, and Maria, but now his memories were telling him a different story, one where he and GUN worked together to protect the people of the ARK.

"Damn it! What does it all mean?! These memories… The Doctor's actions and words… Nothing makes sense!" Shadow looked down at his hands, which were trembling. "Was it real?"

The sounds of a jet propulsion system prompted Shadow to turn around. There, he found a large GUN mech facing him. "It's been a long time, Shadow," the Commander said from inside the mech's cockpit.

"Who are you?!" Shadow asked, taking a defensive stance. "And how do you know my name?"

"I know you… Shadow the Hedgehog! You killed everyone I loved… My family… Maria! I've been waiting all my life for this day!"

"What?! Me… and Maria?"

"Maria was like a sister to me." The Commander's hands trembled. "She was the only family I knew! I witnessed it all… The plan to create that horrifying evil creature, that that Black Creature and insane professor unleashed!"

"So the Professor created me… with Black Doom?"

"You don't fool me! Thanks to you, everyone I knew and loved was killed when the ARK was destroyed! Worst of all, my family! Finally, justice will be served!"

The Commander fired an energy beam from the mech down at Shadow. The hedgehog swiftly evaded the shot and ran around Diablon, jumping up to attack it, only for his kick to be deflected by an energy barrier. "What?!"

"Your attacks are meaningless! This is GUN's latest accomplishment, an advanced mech unit that is one-of-a-kind!" The Commander swatted at Shadow, knocking him back and sending him flying against a wall. He fired another laser, but Shadow managed to recover and avoid it. "This is the end of you, Shadow the Hedgehog!"

Shadow pulled out his pistol and fired at Diablon, but the bullets bounced off harmlessly. As he wondered how he could get past the mech's defences, his eyes caught movement through a nearby window. Looking outside, he found Doctor Eggman leaving the ARK and heading over towards the Black Comet. "That's-"

"Don't you dare turn your eyes away!" the Commander shouted as fired another attack. "You face justice head-on, and repent for what you've done!"

Shadow used his spindash to avoid the attack, and as he did so, he noticed something. For just a moment, the Commander's energy barrier was down. "I see, so that's it."

"Hold still, you devil!" The Commander slammed the mech's hand down, trying to crush Shadow, but he dodged aside.

"Damnit, I don't have time to waste here!" he shouted, and watched closely as he waited for the Commander to strike again. Another laser attack came, and as it did, Shadow saw the shield go down. It wasn't enough time for any normal person, but for the Ultimate Lifeform, it was more than enough. Dodging the attack, Shadow jumped towards the mech and delivered a powerful kick to its floatation unit.

Diablon fell, now hovering only mere inches from the ground. "Urgh! Damn you! I'm not going to hold anything back!" The Commander pulled the mech away as electricity began to discharge all over it. "Anti-matter cannon, fire!"

Shadow gasped as he watched the blast making its way towards him. He turned and skated as fast as he could, narrowly making outside of the blast radius.

"Energy charge commencing. Just you wait, Shadow!"

Shadow charged Diablon, this time baiting the Commander to try striking him with one of the arms. He did just that, raising one of and attempting to grab the hedgehog. As he did, he left himself open once more, and Shadow took advantage of that to fire on the cockpit. He caused some damage, but the glass was reinforced and wasn't going to break so easily.

As Shadow landed, the other arm caught him by surprise and pinned him to the ground. "Energy charge complete! Now it's time to end this!"

Shadow tried to free himself, but the mech was putting its full weight onto him, keeping him trapped. He gritted his teeth and began to glow red as the rage built inside of him.

"Anti-matter cannon, FIRE!"

As the Commander unleashed the devastating attack, Shadow pushed against the mech's hand and freed himself. "CHAOS… BLAST!" Shadow's own attack met with the Commander's, and pushed it back, overwhelming the mech's systems and forcing them to fall offline.

"No!"

Shadow jumped on top of the mech and punched his way into the cockpit, shooting up the controls and causing the mech to lose control.

"This can't be!" Tower cried as Shadow jumped off of Diablon, landing some distance away. The mech lost all power, and fell to the ground, completely lifeless. "R-Reboot all systems! Damn, they're all-" He gasped as he saw Shadow approaching him. Reaching for his sidearm, he opened the hatch and scrambled out. "S-Stay back!" He fired, and then Shadow was gone.

As he looked around for the black hedgehog, a voice from behind startled him. "If what you say is true, then I will respectfully accept my fate."

Tower turned around, pointing his gun at Shadow. However, as Shadow looked into his eyes, his finger eased off the trigger. Those stern yet gentle eyes, full of resolve… 'Maria?' Shaking the thought away, Tower told his hand to pull the trigger. However, his hand trembled. He knew that Shadow was lying, he had to be. And yet, something in Shadow's voice just… didn't sound right. "You mean to tell me that you really don't remember a thing?"

"But I just need some time," Shadow continued, turning and walking away. "To uncover the real truth."

As the Commander watched Shadow leave, he felt his heart beating faster than ever before, his legs trembling, and his resolve crumbling. Shadow was the monster who killed everyone aboard the ARK, so why was he now just walking away, sparing the Commander's life? Was it another trick? But then, who was even around for him to fool? It was just the two of them…

Tower thought back to that time, fifty years ago. That horrible day, when GUN troops suddenly stormed the ARK. Everybody was scared at first. All the patients and doctors were ordered to evacuate down to the planet. It would only be two days later that GUN revealed the reason why, and why he was unable to find his parents or Maria in the crowd.

An accident had occurred aboard the ARK. Unbeknownst to everyone, Professor Gerald Robotnik was using his research grant to manufacture weapons of unspeakable horror, weapons that were deemed human rights violations! There was a containment breach, and his experiment killed everybody in the restricted section of the ARK. All the researchers… and Maria. The only member of Gerald's team that survived, was Gerald himself, who had been on the planet that day, reporting to the government.

The mad scientist was arrested, tried and executed for his crimes against humanity, and that was the end of it… for all but the young boy who had seen Gerald's horrific creation first-hand. Little Abe Tower was the surviving member of the ARK incident who knew Gerald's deadly experiment as more than just an unfortunate accident. He had seen the face of the vile, disgusting monstrosity that had taken his family from him. His foster parents believed he was just making it up for attention, and his therapist believed there were nightmares fabricated to try to make sense of all that happened.

Fifty years later, Tower would have positive confirmation that that monster did exist, when Shadow broke out of Prison Island, where he was being contained. Now, he had the chance to finally avenge his parents, Maria, and everybody else he had lost. But that face… that voice… and those actions. Nothing was lining up with what he was expecting.

"What is this? Why am I doubting myself, after all this time?" Tower asked as he fell to his knees, staring down at the floor. "Shadow… The ARK… Was everything that happened that day really as it seems?"

A long time passed in silence, before a voice called out to the Commander through his radio. Slowly, he got up and approached the fallen Diablon. Reaching in and taking his radio, he answered, "Commander Tower here."

"Commander?" It was the President's voice. "Are you hurt? You sound kind of…"

Tower cleared his throat, standing tall and answering with a firm voice, "I'm fine, Mr. President. I've uh, been unable to locate Shadow, or the leader of the Black Aliens."

"I see. Commander, we have a situation down here. The Black Aliens are approaching GUN Fortress and in large numbers. Your troops are scrambled and I'm co-ordinating them as best I can, but we need you down here."

The Commander sighed, slapping himself internally. How could he have been so blind? While he was so focussed on getting his revenge, he left his soldiers to fend for themselves without appointing a clear leader. Heck, he'd left the President alone in the middle of a crisis! All for the sake of carrying out a personal vendetta…

"Of course, I'm on my way back now. I'm… sorry for abandoning you, Mr. President. Rest assured, I'll be there soon."

Ending the transmission, Tower reached into the cockpit and pulled out his shotgun. After ensuring it was loaded, he triggered Diablon's self-destruct sequence, taking no chances of it falling into enemy hands.

"I have to make things right," he told himself as he exited the room.

Just want to put a little note here: I've been having issues with this site the last couple weeks. This chapter and the one before it have actually been delayed a bit because randomly I just won't be able to upload documents or manage my stories. In the event this happens again, the chapter will be available on Archive of our Own first: /works/26222575/chapters/63821074