Note: This story takes place after the Archie Comics end, so I do my best to keep the New Continuity Canon intact. This fanfic aims to finally put a rest to the Eclipse the Darkling story that was left unfinished. Enjoy!

It's been many long months, and still, the world celebrated the latest success of the Freedom Fighters in fixing the shattered world. For a long time, the world enjoyed peace without news of supernatural destruction or Dr. Robotnik's next big plan. Assuming he had one, and he always did. But while Sonic and his Freedom Fighter buddies enjoyed their breaths of fresh air, Team Dark remained unchanged and tasked as always.

As long as Eclipse the Darkling and his Dark Arms roam the world, there will be no tranquility for G.U.N. The alien was the last subject remaining from the terrible Black Arms, the evil race set on devouring the world. A long time ago, they were plentiful and powerful and came by the planet on the Black Comet, ready to consume and destroy the universe. When Shadow the Hedgehog defeated Black Doom and the comet with him, control fell to a smaller and weaker group. Another master, Black Death, controlled that one and came back specifically for revenge on Shadow's betrayal of his creator. He created Eclipse as a weapon to kill him, but Eclipse wanted Shadow to join them instead.

Unable to convince his "brother" to come home, they attempted to mind control him, but that didn't work as planned and G.U.N destroyed the final comet. That would have been the aliens' extinction, but Eclipse managed to escape on a shuttle with four surviving Dark Arms, wisps bred with his blood.

Team Dark investigated the place where the shuttle landed, Angel Island. There, Eclipse tried to steal the Master Emerald to become powerful enough to gain a second chance in his conquest. It was a close match, but he managed to escape once again after stealing a G.U.N shuttle. That was the last day Shadow saw the fiend, but his determination rose with each passing day.

"I want all our efforts on finding the alien." Commander Abraham Tower after another attempt of finding Eclipse, only to find the abandoned remains of another hideout. "The longer that thing walks on our earth, the more danger we are in."

The big screen taking up the entire wall beside the stoic man changed to show a map of the continent and where every G.U.N group was stationed during the time when the world was still shattered. "Our forces were thin before when so much of the world needed G.U.N.'s assistance. Now that problem's solved, I want every able agent on the field looking for that alien. From what the records show, we are going to need everyone to finally catch this beast. Despite finding its previous hideouts, it always managed to slip out of our grasp. Men, we are going to need more teamwork and solid plans from now on."

Rouge's focus on the commander's stern words dissipated as she noticed Shadow shifting in the seat beside her. He growled under his breath. "Every moment spent here is time we could have hunting Eclipse."

She couldn't help but scoff in response. Her friend was certainly giving his all in this mission. Maybe too much. It was no surprise at how hard he worked on any mission, let alone such a personal one, but even the Ultimate Lifeform has limits. He was never a heavy sleeper and he always preferred to eat on the run, but since the world reformed in one piece, it seemed Rouge was the only one grabbing coffee in the break rooms or even meeting the other teams during mealtimes. Most of the time he didn't even bother to show up long enough to grab something and leave. The longer this went on, the more he seemed to forget his needs. She pondered if this would go on long enough to see him collapse, and what good would that be to anyone?

Talking to him about it would be useless. She and Omega may be the ones he trusted the most, but even then, it's always hard to make him see reason. The only thing they could do is assist in bringing down the alien one way or another.

"I want as many teams responding to a call on its location as possible. Every time. Team Dark will remain the head team during this mission as they know the fiend the best and can sense when the alien's nearby," Commander Tower held an open palm to the three seated members in the audience. "I want them to have authority over the actions of the other present agents." He paused long enough to take in any response the teams may have as he moved his arms behind his back. Several of the teams didn't have high opinions of Team Dark. It was no surprise. The majority of the teams were human, and the three members of Team Dark all had suspicious backgrounds, not to mention they were the agents with missions of the highest importance and often the highest success rates. That brought about some unlikely competition and jealousy from others. After seeing no one objected to his orders he nodded and gestured to the assistant presenter to turn off the screen. "That is all."

Chairs scraped the floor and the chamber filled with murmur as people left the room. The hedgehog marched behind the crowd of tall folk. He didn't pause or even look at his companions as they joined him. "Here we go again," Rouge remarked in a light tone. "What number of hideout will this next one be? Five hundred? Makes you wonder how many people he encountered or threatened. I half expected to run into Sonic's team at some point."

"We don't need their help." Shadow returned, unchanged. "Eclipse has nowhere to go. He will tire eventually."

"Of course he will." The bat responded, working hard to keep up her pace to stay at his side. "And I'm sure he knows it too. There're only so many alien plants he can leave behind, hardly having enough to harvest. If we don't capture him soon, he's going to turn around and strike us."

Silence floated in the air as the dark hedgehog rounded the strategy table, currently displayed with all the areas where Eclipse stayed or was spotted at some point. A few humans followed them into the room with their own discussions. Shadow leaned over the surface and finally looked into the faces of his teammates. "Omega, is the Ark close to narrowing down Eclipse's bio-signature?"

"Scanners are attempting to narrow down a location within 700 miles." Came the booming reply.

Shadow's gaze fell on the map under him. "He can cover a lot of ground in a short amount of time, but he can't keep running. What could he be looking for now? He's too smart to go back to Angel Island for another chance at the Master Emerald, but what other hope can he carry at this point?"

Rouge copied his lead and planted her gloves on either side of her on the image in the glass. "I don't think he has any, but he's too stubborn to give in. Like you."

Shadow ignored her comment. "There's only one thing I can imagine he would go for next."

Rouge could answer that thought in less than three tries, but she played along. "And that is?"

"The Chaos Emeralds."

Of course. The seven Chaos Emeralds are not as powerful as the Master Emerald, but it was one of the Black Arms' major goals from the start. Eclipse had all the same information that Black Doom had. He would know about the power of the emeralds.

Still leaning over the map, Shadow lifted his gaze to study that of Rouge's while he waited for a reaction. She couldn't decide if there was a particular response he wanted her to have or not. "They could be anywhere now after Super Sonic used them to fight Dark Gaia. Would he really scour them while risking losing any to us? An Emerald's signal wouldn't hide him. If anything, he might draw more attention to himself."

She already knew the answer would be a simple one before Shadow spoke next. "He's also sensitive to their power, and as you said, he doesn't have many choices left. He can follow their signal if one's nearby, and even with G.U.N. on our side, it may not be enough if he utilizes that power. With all emeralds, he will be able to destroy the world."

"So, you're saying we need to find them first."

Omega slipped in before they could discuss it further. "Previous experience with the alien versus power statistics show our best chances to overwhelm him is in the number of forces against him. It would be unwise to split units to search for the emeralds."

Rouge pointed at the robot. "Ha! So, you're saying you're too weak to fight him after all, huh? Guess it only takes two defeats from a little alien for the Great and Powerful Omega to admit he's not the stronger."

A few clicks and whirls disagreed immediately. His large, chunky body turned to face his teammates. "Irrelevant," he barked loud enough to silence the chuckling humans behind his back. "I do desire another chance against the alien, but I demand a one-on-one. I only failed our last encounter because of the power his minions provided him."

She still couldn't help but laugh as she came around the table. She patted Omega's arm as she passed him. The solid metal sang a little clank as she did so. "If you say so, Tin man." With her palm still on his upper arm, she planted her other hand on Shadow's shoulder, who went back to studying the map. "What's the plan, boys?"

Shadow didn't even take a breath to answer. "We find him before he lays his hand on an emerald. If he's near one when we find him, we take it first."

"I should have known," she sighed.

Her hand slid as he moved away from the table and walked to the door. Omega's head turned to accept Rouge's silent gaze. Staring into the optic sensors of a cold war machine didn't weaken the bond she had with her robot companion. She knew, despite his stubbornness, he felt the same. Through their union as a team, she believed the three of them would come out of this all right. They always have before.

...

Julian Snively lingered by his worktable, pretending to study something important in his magnifier until the halls fell quiet. He counted twenty minutes of uninterrupted silence before lifting his head and observing his science chamber. Not a soul in sight. The door remained open and undisturbed. A wide grin appeared between his thick red mustache and beard, and he crept to the large screen computer behind him.

He gave the open hallway another cold look as he fumbled in the pockets of his lab coat for a jump drive. Having located it, he paused again to look up at the clock near the ceiling. Nearly midnight. He scratched his bald head and hesitated one last time before sliding in the jump drive and turning on the screen. He would be a lot more focused if he could close that dang door. Maybe even lock it, but he would not dare entertain the thought further. Even just closing the door could alert the C.L.I.P Division to suspicious behavior.

He growled and logged into the computer. The keys click-clacked in protest as he pushed each one down hard. If Madonna Garnet watched his moves any closer, they would be handcuffed together. Every time he saw her spying on his business, his files, it made him want to rip his hair out, but in the end, he supposed it didn't matter. He had a solid story. They knew he worked for Eggman in the past. He convinced them he did so undercover so that G.U.N. would know more about his strategies. And the situation on Angel Island? Dr. Snively only ordered what he thought was best for the safety of the Master Emerald! Everyone agreed they didn't want the alien to have it. Why would anyone assume Snively wanted the power of the Master Emerald for himself? They can't prove anything.

Within the secret files on his jump drive were the plans for Operation: Conquest. Even though Commander Tower believed he was hiding something nefarious, Snively still had complete override controls on the Space Station Ark and satellites in orbit. That was already two-thirds of the power he needed to control the universe. It's too bad Team Dark didn't bring the Master Emerald back to G.U.N. That would have been a lot easier. It would have been right next to him! Now, he would have to revert to working under the radar and take it without anyone knowing. This time, however, would be even more difficult than before. Not only was Snively under close watch, but so was the Master Emerald. The alien's attempt at taking it had the organization on edge, and that's not to mention the watch its overprotective guardian had on it, especially in times like this.

Knuckles would have been hard enough to sneak around, but this latest attack... Whatever. It was still on the island. All Snively had to do was formulate a plan to get to it without the C.L.I.P Division jumping on his back. He had time. He had all the time in the world, and if the alien attacked again, he could use the distraction to his advantage. Everything will fall into place. He only needed a little bit of patience.

...

Every radio around her blazed in alarm. It happened so fast. Before she could even process it, the station-wide message of Eclipse's approximate location had Rouge bounding out of bed. Instinct drove her all the way through the equally tired but active G.U.N agents and into the ready transport vehicle. It was when she finally found a seat beside her giant robot friend when her senses caught up. The door of the truck slammed close and they began to move. "Where are we going this time? I think I was sleep-running all the way here and missed most of the message."

Omega remained still with his claws on his legs. "The eastern edge of Frog Forest. There's a 90% chance the signal is Eclipse and his minions."

Rouge groaned and stretched her arms above her head. "Nothing better than a late-night alien hunt. What time is it even?" She ended with a yawn.

"3:26 AM," Omega replied.

Rouge slumped for a moment. The seats were not uncomfortable in any way, but they, and the steady movement of the vehicle, brought back the wave of exhaustion she shook off when she hurried out of bed. Looking back on her rush that moved like three seconds in her mind, she realized the sirens drove them all into a bigger panic than usual with these signals. "Let me guess, a signal for one of the Chaos Emeralds was near his location."

"Affirmative."

She rolled her head back and sighed, crossing her legs. "He's going for them after all." Sitting back, she took in the rocking and crushing of the terrain. Every now and then, the driver and his passenger answered and carried messages over the radio to some of the other teams. Everyone in the back kept to themselves. None of them looked happy to be woken up either. "Where's Shadow?"

"He'll meet us ahead."

"You've got to be kidding! He plans on running all the way there?! It's a long distance even for him and he knows he stands no chance against Eclipse on his own!"

Omega's head whirled and turned to her. "He's worried about the Chaos Emerald. He may be trying to get a head start on reaching it."

Rouge threw her arm in the air before slapping her hand down on her face. "Ugh! I can't believe him sometimes."

Omega didn't seem as perturbed as she did. "If he doesn't run into any problematic encounters on the way, he has a good chance at reaching it first."

If he was trying to convince her it was better to have Shadow run ahead, it didn't work. "Yeah, if he doesn't die to Eclipse before finding it!"

"I only find it a pity we can't go with him. I wanted to reach the alien first."

Rouge folded her arms when she picked up the spark of the robot's usual excitement for violence. "Oh, I'm sure we will have plenty of action when we get there. I imagine Eclipse won't flee as quickly this time. Not when he's trying to get away with a Chaos Emerald." When the conversation fell flat, she decided to ride the rest of the way in silence, attempting to squash the impatience rising in her belly. It was going to be a long night.

It was even longer for Shadow. The hedgehog tried his best to rest that night before the alarms took off, but the taunting voice burrowing in his skull reminded him why he shouldn't bother trying. You can't deny your lineage, the terrible voice of Eclipse stated. In his mind, he circled him like a shark, giving him no escape. You belong with us. To deny that would be to deny your very existence.

In reality, his room remained still and almost peaceful in the dark, but to him, there was someone he couldn't see in the room. He could feel the misplaced air around the invisible figure hiding in the dark. Like always, he attempted to chase away the illusions by turning over on his other side. It didn't work. The voice was so sure of itself. That made it worse. The further he tried to bury himself beyond Eclipse's reach, the further his words echoed in him. His reasoning was... Painfully logical. Shadow never belonged here to begin with. Not on the planet and not on the Ark. It was the blood of the Black Arms that made him the Ultimate Lifeform. Ever since he was created, the people here feared him.

No, that wasn't true. Somehow, he found trusting companions in this world, even when they knew exactly what he was. Rouge, Omega... Maria... Stop pretending! The voice yelled in his ear. Shadow shot upright and the visions finally dissipated, but that didn't bring him any relief.

He's not in your head, Shadow answered back to himself. You may not know where he is, but you do know he is too far away to mess with you. He knew if he lay down again, it would only start all over, so he sat under soft sheets for a long while, taking in the room. If it wasn't for the soft wind outside and his own stressed breaths, he would be in complete silence. No one was in the room with him. The dark corners weren't even as dark as he perceived a moment ago. His eyes stung. He brought this torture on himself, but why? He knew why, but he dared not face it. Staying in that room any longer would only bring those visions back, so he left. The sound of the alarm brought him another chance to put an end to all this. By reaching the emeralds first, they could stop Eclipse sooner. Shadow was the first to leave after he hurriedly told Omega to meet him there.

Now he raced to his destination. Every minute and every hill took him closer to Eclipse and the emerald. He will reach the emerald before it's gone, but he may not be able to avoid Eclipse for long. That means he may have to fight before the others get there. It also meant there may be a chance for Eclipse to manipulate him again. Shadow clenched his jaw and refused to slow down. He couldn't let Eclipse slow him down. He will reach the emerald first if he faces the alien or not.

More and more trees dotted the hills. Shadow charged head-on and accepted the lush forest to swallow him. No turning back now. A little more northeast. Obstacles became more frequent and large mushrooms and vines forced him away from his path. This was just how he remembered it. Frog Forest was more of a jungle with its overgrowth. The hedgehog slid, turned, and skated off and on vines without missing a beat. A sea of croaks warned him to keep watch for the frogs with the ability to change the area's weather. This time of night, he should expect to see many. G.U.N may have a harder time coming through here. All the better Shadow decided to run ahead. If he relied on them, the emerald could be long gone by the time they arrived. Who's to say Eclipse isn't already there?

Luckily for him, that part of the forest was like the rest of it; humid and green. Well, it would be a lot greener in the day. The light of the moon made it appear a lot more turquoise. The spots of grass where the clouds covered made them nearly invisible. Shadow came to a halt and surveyed the landscape. Mushrooms, giant trees, rocks, and dirt kicked up by the inhabitants of the forest. Now that he stopped, he picked up the singing of the crickets adding to the still rolling croaks. If it wasn't for a distant trickle, he would have thought the scent of moisture meant it rained here recently. He closed his eyes for a moment but sensed nothing else. He was the only one here. At least, for now.

The emerald was here too, on the edge of the forest, but there were still so many places to search. It could be buried in the dirt or stuck in the top of a tree somewhere. Shadow hoped with a bit of luck he could see it reflecting light back at the moon. Because of that, he decided to go through the area quickly before searching more carefully. He decided to start on the ground floor.

That was his intention at least, but more giant frogs began emerging from behind trees. He may not be able to plan any strategies for this search if he wanted to remain hidden. Unfortunately, avoiding these creatures would be a lot harder at night... Not much concern for the dark hedgehog, but a nuisance regardless. He kept to the foliage whenever possible and moved without making a sound. Still hidden and hugging cover, he tried to spot areas of interest. Then, the moon lit up more soft ground. The dirt mounds made the ground uneven and obstructed his view. Looks like that may be a good spot for an emerald to land... He crept closer.

He almost made it to the first mound before he had to duck into the nearest bush again. Frogs. Three of them. They hopped close together where they croaked softly to one another and looked at the stars. It didn't look like they were leaving anytime soon. Looks like he won't be able to search there himself, but maybe he can view a different angle of it. Shadow waded further into the bushes where he stopped at the nearest tree, taking a vine up. He crawled along a branch overlooking the area of soft ground. Nothing. Just frogs and dirt, but climbing the tree was not a waste of time. The angle he looked from allowed him a good view of the surrounding areas. If this forest wasn't so overgrown, he would have even more to see where all the tall trees obstructed his view. If he climbed to the very top of the one he was in, maybe he would be able to see beyond more of them.

He backed up and reached for a branch above his head but froze. When Shadow came back out on the branch, he saw it glimmer again. Near the spring a little past the dirt mounds, the moon shown down on a clear gem where it shimmered like a small beacon.

Careful still not to alert any frogs, he dropped from the tree. The spring was level where he was now, though there was a deep slope between them. He came to the edge of the hill and slid down. The Chaos Emerald was barely in his sight now, but now wasn't the time to be brash. There were more frogs resting nearby. He kept an easy pace for the slope where he could make out the facets in its shape.

Looking for something, "brother?"