This story takes place right after Sonic Universe 70. I highly recommend the Archie comics! Eclipse's story spans from issues 59-62 and 67-70 (he appears briefly in the story from 63-66, you don't have to read those, but they're fun anyway so). Don't worry, you don't need to read ever single issue before those to understand the story. Enjoy!
Mystic Ruins was once home to an ancient civilization of Echidnas. It had also been the base for one of the infamous Dr. Eggman's schemes thousands of years later. Nowadays, it was a quiet jungle that was mostly uninhabited save for a Mobian cat that liked to fish and his best friend, a frog literally named Froggy.
The Mobian cat eyed his friend, who hoped around restlessly. He then turned to the fishing pole in front of him. It was completely still, they'd only caught a single fish that day.
"Are you alright, friend?" The purple cat asked gently. The frog made eye contact then hopped back into their small home. "Oh, well you could have just said you were tired. It's okay."
The cat got up and reeled in the empty bait. He was about to place his fishing rod in its usual spot outside when he saw a sudden flash of light in the sky. He glanced up to see an apparent flying contraption fly aimlessly close by. He heard a rather sudden, loud crashing sound and proceeded to grab his fishing pole and investigate.
As he went, his frog friend looked at him from the window and although the fisher waved at him he noticed his friend was reluctant to follow. After a few pleading looks from his friend, he caved in and joined, albeit with a worried expression.
Maybe it was just a lost explorer. Perhaps their gear went haywire on them or something. He didn't think it was anything to worry about. He doubted Eggman would come back, he had so much going on with the Freedom Fighters finally getting the planet back together and everything. It had been peaceful since the dark gaia creatures stopped showing up, so this happening was really random and out of place.
As he and his companion drew nearer to where the flying carrier landed he saw smoke coming out from the clearing and torn trees from where the landing was rough. He made it to a swamp like area, mud everywhere from the constant rain lately. His ears perked up when he saw that the flying contraption had a 'G' symbol adorned with stars. It was a G.U.N. carrier!
"Let's hurry, see if they need help!" He ran towards the wreckage with his companion cautiously hopping behind.
"Augh… w-where... ? Where a-am…" Eclipse woke up dizzy with vague pictures flashing in his mind of what had just happened before he passed out.
Please be okay! The last words echoed in his head followed by what he remembered was an attempt at holding on to the Dark Arms while they frantically cried and panicked as their ship was going down a second time… not that they could remember the first.
The alien immediately jumped to his feet, although unsteady due to a few bruises, and began looking for his wisp hybrids.
"Little ones? Dark Arms, where are you?" He called after them, looking near the cockpit and main command room. He searched nearly everywhere, breaking and turning over any and all old equipment used previously by G.U.N. and Team Dark.
"Blurk! Cregal! Cyzer! Rhygenta!" Upon reaching the back of the shuttle, intended for cargo, he was getting desperate. The shuttle was partly on fire, still, and none of the Dark Arms answered his calls. He kicked open the main door revealing the dusk and wilderness outside. He ran out, mud staining his clawed feet and legs. He shouted their names again, not caring if there were G.U.N. soldiers or anyone else that could possibly hear him.
He panicked at the thought of what had happened just a few weeks prior… When he'd crash landed his own ship into the mountains….
No, no, no…. His legs crumbled as he fell to his knees and buried his face in his clawed hands. Not my children, please no….
A flashback came to him packed with images of the wisp hybrid eggs cracked and oozing blood. He could have easily given up that day. The one thing his master had asked him to protect fiercely was the next generation… but only his four darklings made it out of what could have been hundreds of Dark Arms fueled with desire for revenge.
He still thought about them. Just like he'd still think about the members of his race and his creator, whom he deeply regretted never listening to.
"I've always been a crappy pilot, now turns out I'm a terrible leader, and father and… I'm sorry, master..." He choked through tears.
A few months ago, aboard the Black Comet…
"You know, Black Doom had no say in giving his traitorous son free will," Black Death reminded him.
"I know… I know, you've said this already, like what, five times?" Eclipse rolled his eyes.
They were in the Dark Arm's nursery, and he was tending to the eggs until his master's eye had arrived, with talking points already discussed.
"And most Black Arms agree that was his biggest mistake," he continued, "not demanding to that human, Gerald Robotnik, that Shadow be created by our standards."
"... Right…" Eclipse said, uneasy. "So, then... what?"
"So then what, what?" His master repeated, clearly irritated.
"So then why are you telling me this again?" Eclipse demanded, turning to him, "I get it! I annoy you! I wasted your time making you turn the Comet to Planet Wisp, and I get on your nerves every time I suggest Shadow can be redeemed…"
With restraint anger and tears he added,"...you regret making me, don't you?"
Black Death's eye stared down at him quietly. Then, it flew off and disappeared into the door… as Black Death himself arrived. Eclipse tried to quickly wipe his tears, and turned away from him, awaiting a scolding for his outburst.
"... No, I do not," the alien finally said, "but you didn't let me finish."
Eclipse couldn't look at him. He didn't want to hear this. He spent his life cherishing and respecting his fellow Black Arms only to recently be told that his entire purpose in life was to kill one. And not just anyone. One that had free will and a single purpose. One that functioned just like he did.
"I don't agree that Shadow's flaw was that he could do what he wanted. I think the problem is that he knows nothing about his heritage, and thus, despises it because the humans had taught him so."
Eclipse timidly lifted his chin to face him.
"When I see you, I realize what Black Doom's son could have been. Yes, I find that you are naive and irritable…" Eclipse crossed his arms and pouted at that comment.
"... But you are young." He said softly." I also notice that every time you defy me, you genuinely believe it is for the betterment of the Black Arms.
"I take notice in everything, from the way you interact with my soldiers… to the way you protect the infants… you care about this, and although I don't think there's a shred of that in Shadow, it moves me to know Black Arms don't inherently need to be stripped of their will to care for each other. Black Doom didn't believe in that, because during his many visits to Earth, he would retell of wars and battles the humans would fight against each other. He hated the thought of our species ever turning like those savages… but now… I see you, and I know we're nothing like those humans."
"... Oh." Eclipse looked down again, his pale cheeks took on mild blue hue despite feeling so warm, "I-I'm really sorry, Master, for being so insultingly ignorant and accusing you…"
"It's fine. I've been harsh with you lately, but I think it's important that you recognize that you still play a role in the hivemind, Eclipse. You're a soldier, foremost, and I know that you're doing because you care, but just for once ..."
The ancient alien held up a finger warningly.
"Don't. Shadow won't change. He's betrayed us, he's not worth it."
He looked around at his surroundings. He didn't have trouble looking through the dark, but his vision was blurry from all the crying. He got up, his knees also stained with mud now.
It wasn't going to end this way. Not right now. Not like this.