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Published:
2024-05-01
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2025-09-12
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14/?
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Beyond Instincts

Summary:

Sonic's not desperate enough to be interested in some pawn of Eggman's. His impending heat may be influencing his moods but certainly not his rational thinking.

He really, seriously isn't interested.

But Shadow obviously has more layers than he lets on and Sonic has never been able to stop himself from trying to help those in need.

They were always bound to clash.

--

In which one of Tails' solutions is to link Shadow with Sonic to prevent Shadow from obeying Eggman but that goes as well as you'd expect.

Well, at least they get to show Shadow what being a pack is all about.

--

(Updates inconcsistent)

Notes:

HELLO ITS TIME!! I've yet to finalize the amount of chapters this is gonna have but I'm estimating around 20 at most.

Now if you notice any plot holes-- please forgive me, this is my first official fanfic that has branching plot points and I'm trying my best haha
If there's anything unsatisfactory with my writing, sorry but I HAVE TO GET THIS OUT OF MY HEAD or else It'll haunt me forever! So for those that aren't bothered by some imperfections, please enjoy my take on the omegaverse!

(See the end of the work for more notes.)

Chapter 1: First Impressions

Chapter Text

Ah yes, night time.
Known for the moon and stars casting its gentle glow to where it could reach, the soft rustle of flora that is a result of the salty ocean breeze sweeping past and the faint snores that come from (‘creatively’ called) ‘Greenhill Village’.
Where various and unique packs rest inside their warm comfortable homes, with a few night-owls (some, literally) still awake doing what they do without a care in the world–

Hence ignorant of the battle happening this instant for the village’s safety. A spontaneous decision, really.

Deep within a forest connected to the village by the giant loops, “I’m telling ya Eggman–” there is a certain hedgehog that appeared like a streak of blue as he used his sharp quills to its full-potential. Bouncing from one badnik to another with a swift calculated spindash.
Shortly after, he lands on the ground, his foot sliding through the dirt in one smooth sweep, “CRASH CRASH CRASH” while badniks dropped-dead in a not so elegant fashion. As a result, innocent critters DART away the moment they are freed from their mechanical confides.

Sonic shows his victorious signature-grin to the doctor who, like usual– stayed inside his floating-mobile that resembled an egg. “Just GIVE UP!” Sonic taunts, the dirt that stuck to his peachy fur brushed aside.
He puts his gloved hands on his hips, “Aren’t you tired of having your poor walking-tin-cans destroyed every.single.time?”

Far from amused, Eggman slams his hands on the poor vehicle that stumbled from the force. “Am I Rat!?” Eggman spits out, something that Sonic snickered at. “I’ll see to it that you die of exhaustion!”

“Woah there–” Sonic raises his hands in the air, shaking his head. “Don’t get ahead of yourself, we both know you’d pass out first~”

Eggman does a grabbing motion in the air, likely visualizing that it was Sonic’s neck before eventually, he slumps down.
That is Sonic’s cue to expect some more bots to show up and so he adjusts his stance accordingly, a cocky smirk on his face. Yet as seconds passed with Eggman’s head still hanging low and hands gripping the edge of his egg-mobile tight, a small knot forms in Sonic’s stomach… smile dropping.

A sense of foreboding hit him, instincts somehow urging him to run away.

“Is that so???”
Sonic jumps back in alert when Eggman finally talks, tone strangely confident and mocking.
“Clearly, you need a new ‘playmate’. Not another one of my many ‘tin-cans’~”

Sonic frowns, an eye-ridge raised at the direction Eggman was taking them to; hinting something bigger than the usual badniks. Sonic’s ears twist to listen into his surroundings but pick up on nothing special, just the usual sound of swaying leaves and the wind… it only served to make him more wary.

Someone that can keep up with you and dare I say– beat you in all aspects.” Eggman’s monologue did not help in the slightest.
Last time Eggman was like this, Sonic had to fight a gigantic badnik that was dead set on destroying the village.

“All the more of a reason to be grateful for my surprise, blue-pest!” States Eggman with a crazed laugh, arms spread in the air.

…Was that supposed to be some sort of signal? Sonic couldn’t tell because even after a minute passed, there was no supposed ‘surprise’ lunging at him…

Foolishly lowering his guard, Sonic scoffs. “Sounds like empty promises to me Eggma–aaAACK!?” Alas the second he blinked, he is flung to a tree– back slamming against the trunk as golden rings popped up from him.
He gasps for air and squints his eyes open through gritted-teeth, glaring at the figure shrouded by darkness towering over him, nearly blending in with the night if it weren’t for their red-stripes along their black fur and the white chest fur.

A hedgehog with a metal collar…?

“HOHO!” Eggman’s laughter booms and scares nearby critters away, the doctor circling above him as if to celebrate.

Sonic attempts to stand up but is pushed back down onto the trunk by the foot on top of his heaving chest, metallic shoe feeling strangely warm and heavy.
He grips the bastard’s ankle that has some sort of golden ring for an anklet, trying to pry the foot away but with every pull he does, the harder his new ‘friend’ pushes down– quite literally, stealing his breath. A disappointing experience when all Sonic wanted was to experience the romantic-kind but he guessed that’s too much to ask for with his hectic lifestyle.

Like Eggman was introducing a new pet to his old one, “Shadow! Meet Sonic!” His tone is sickeningly sweet.
“Sonic– meet Shadow, The Ultimate lifeform!” Then he lowers his voice to a menacing degree to emphasize the newcomer’s title.
If Sonic wasn’t busy glaring daggers up at this so-called ‘Ultimate-lifeform’ who didn’t even look back at him and instead stared up at Eggman, he’d certainly have rolled his eyes.

“Now–” Eggman clasps his hands together, “Play nice~” he sings as he slowly ascends higher and fly deeper into the forest and leaving the two hedgehogs be but he’d be an idiot if he didn’t expect Sonic to chase after him, that’s probably what Shadow is here for isn’t it...

Leaning forward with all his weight, Sonic rolls and pushes Shadow off who’s back meets the ground with a loud thud, a quiet groan following after. Sonic doesn’t give him even a second to stand up, immediately pouncing to pin him down by the wrists decorated with golden-rings down to the ground.
“Sorry, I’d love to ‘play’ but my target is whatever Eggman’s trying to do so if you’d just stay down for a good minute-” Sitting on top of Shadow’s torso, Sonic is about to slam his heel down Shadow’s head to knock him out yet Shadow disappears– his butt meets the ground and his hands suddenly lack the wrists he held on to tightly moments ago.

This time, the sudden smell of antiseptic(?) from behind him alerts him to duck. “OK! WOW– Teleporting!” He loudly exclaimed as Shadow’s kick barely grazed his quills, realizing the other’s ability which answered a lot of questions.

So this guy is better than the usual minions Eggman sends out, no big deal.
“Jokes on you bud, I’m fast!” No matter how strong Shadow is, as long as Sonic’s faster– “SEE YA~!” Then he can leave the guy behind the dust that forms as he sprints to where Eggman headed off to.

The hero takes a deep breath, welcomed by the familiar force that is the cold wind swaying his quills, fur and brown scarf. Chaos, he sure took breathing for granted… He’ll be sure to ‘repay’ Shadow some other ti–

“What the–”

Still running through the forest without any problem looking ahead, his green eyes are glued to a particular hedgehog skating BESIDE him, a blue and yellow trail running side by side.

Now the discovery that another mobian is just as fast as him would have made him cheer! Maybe even challenge Shadow to a race or be excited overall that there’s someone that could actually keep up with him, except… This is his enemy.

Surprisingly, sharp-eyes lined by the color red finally focus on him–narrowing while a smirk makes its way to his tanned muzzle. “So am I, hedgehog!” Are the first words Shadow yells to Sonic, gruff voice sounding ‘feral’ with the way he growls as he picks up his pace, definitely a competitive sport; probably an alpha...
Shadow glides towards him in an effort to slam him down to the ground but Sonic leaps forward before he could.

“Didn’t think you talked!” Landing on top of a branch, he first waits for Shadow to be directly beneath him before he descends and aims a downward-kick that Shadow narrowly avoids by leaning to the side.
“There’s nothing to say to you,” Shadow replies, delivering a nasty-left hook towards Sonic’s temple which Sonic dodges by arching his back.
“But you just did!”

At this point, they exchange blows utilizing both their arms and legs– neither show signs of taking the lead, surprisingly on equal ground even though Shadow’s moves were a bit more ‘rusty’ judging from how he occasionally stumbled. That’s the only reason why Sonic managed to stiffly intertwine his fingers with Shadow’s, shortly pulling him close with a small practiced spin that looked almost harmonious if it weren’t for the scowl on Shadow’s face.

He pounces with vengeance.

Each of their hits are either countered or dodged, navigating through the terrain like they were participating in a dangerous dance, their audiences the fauna and critters watching with bated breath from afar.

There might be some unnecessary flare but would it be Sonic if he doesn’t have a little fun with his situation? It’s rare to find an opponent that actually matches his speed so he felt a bit excited exerting himself, despite the creeping exhaustion for having no prior rest. Not that he let it show, courtesy to his years of experience and adrenaline for keeping him lively!

Initially invested in their fight, “Shadow! Hurry and finish that menace off, I’ve got what we came here for!” Sonic is caught off guard when Eggman’s voice enters his ears, noticing that the madman was steadily approaching them and holding what looked to be the white chaos emerald.

Unfortunately for Sonic, “Guh–!” it’s his surprise that gives Shadow the chance to kick him towards yet again– another tree.
He’s getting real sick of trees chafing his back…

Shadow’s elbow jabs at his peachy chest, keeping him pinned against the tree despite Sonic’s hands gripping the striped arm in an attempt to escape, legs trying to run but Shadow’s strength was surprisingly monstrous and wouldn’t let him move an inch…
His nose picks up on the vague barely noticeable medicinal smell that came from Shadow for being so close, a reminder of his predicament all because he just HAD to look for some sunflowers in the middle of the night for his nest. In spite of the danger, Sonic shows a small smirk to the hedgehog glaring at him, mischievous intent clear.

Tilting his head to give the illusion that he was staring down at Shadow, “If you weren’t trying to knock my teeth out right now, you’d actually look handsome,” he makes light of his situation with a taunt.
To be fair, Shadow is handsome on a surface level, with the way the moon’s light showed his sharp features? Not to mention apparently skilled and strong? Even with the weird peculiar scent? Still a solid 10 in Sonic’s book–
Wait, stop being desperate Sonic, you’re still a month away from your heat! Remember Sonic, this is an enemy.

The taunt actually seemed to have surprised Shadow, eyes widening briefly before his expression morphs into that of someone annoyed, eye-ridges scrunched together in confusion. “...You’d be tolerable if you shut your mouth.” Shadow applies more pressure to Sonic’s ribs, drawing out a small wheeze.

“Get rea–dy then cus’ I doubt… you’d be able–hah– to shut me up pal,” That doesn’t stop Sonic from talking though, albeit he is panting but his smile remains– winking at Shadow with the confidence of someone walking out of this alive, understandable considering Sonic’s track record with these things…
It’s a miracle Shadow hasn’t slammed his head to the tree by now, possibly amused. “Big words for someone cornered.”
Sonic’s peach shoulders shrug, strangely indifferent, “Ehh, this– happens a LOT more than… you’d expect.”

Shadow scoffs. His hands move to grab Sonic’s scarf, harshly pulling the hero towards him.
From how things were going, Sonic braced his face to get hit until he felt Shadow’s grip on him stiffen and freeze in place.

Cautious, Sonic squints his eyes open– Only to see Shadow’s nose scrunched and eyes squeezed shut, tanned muzzle turning red. Confused, he tries to pry the hand gripping his scarf but Shadow abruptly takes a few steps back and so pulls the scarf with him– pushing the back of his palm against his nose as if to block out Sonic’s scent entirely, body slumping to the ground.

“Shadow!” From above, there came an angered roar as if that’d help Shadow get back up on his feet.

“First of all–” Sonic coughs now that he could breathe, rubbing his bare neck almost defensively, “Rude!” then took advantage of Shadow’s discomfort to punch him by the jaw! Sending Shadow straight into the air from the sheer force alone.
As expected, knowing Shadow’s reaction to his scent, the uh– the punch might have been a bit personal.

That could also be why he noticed Eggman’s close proximity late, too busy trying to rationalize the negative reaction amidst his embarrassed rage.
Not giving Sonic the chance to stop him, the eggmobile shot out a clawed hand which grabbed hold of Shadow by the torso, lifting him up from the ground in an instant. Sonic upon noticing and brought back to reality, leaps towards Shadow in an effort to grab the hedgehog’s leg but he misses by just a second, face meeting the ground as he slid across. Recovering fast, he spits out the dirt with a frustrated cough and stands back up.

“Hey! You can’t just fly off!” Sonic yells with fists flailing in the air, jumping clumsy thanks to the number Shadow did to tire him out.
“On the contrary!” Claimed Eggman, floating off with Shadow in tow just mindlessly dangling– Sonic would even describe it as funny-looking if he wasn’t so pissed.

“Damn it–!” Sonic cursed with a slight hiss, wiping his dirtied face. “You’re not getting away with this Egghead!”
Sonic grips his neck, feeling chilly without the usual fabric “And give me back my scarf!”

“I CAN'T HEAR YOUUUUU” The doctor’s childish reply echoes throughout the forest and into the night sky.
Sonic swears he saw a sort of winged-dark-figure following the eggmobile and he would have pondered some more about it but now that there was no immediate threat around– his body breaks down and he realizes that his knees are practically friends with the grassy ground. In an effort to yell out his frustration, all that comes out is a pained wheeze. He grabs his chest– breathing out slow and shallow puffs of air to soothe his aching and throbbing lungs.

Alright… Sonic stands up, nearly stumbling down.
Eggman and figuring out what their plan is plus where Shadow came from can wait. The last thing he needs right now is Tails scolding him for a multitude of (unfortunately) valid reasons. He’s heading straight home before Tails wakes up and hopefully fix himself up no problem.

Spoiler alert; he passes out face-flat on the living-room floor. Sorry Tails.

 

 

Metal as far as the eye can see, they’re greeted by the smell of iron in contrast to the wild-life they were surrounded by earlier. White, gray, black and occasionally a splash of red decorates the entirety of Eggman’s base. Robot-minions sometimes pass them by during their walk through the halls, both their steps creating a chaotic rhythm.

Eggman twirls his stache, a nervous chuckle leaving his throat. “Maybe sending you out immediately was a bad idea…!”
Looking back at the doctor that towered in height, Shadow’s eyes had an intensity to them that made Eggman clear his throat. “You think?” The hedgehog shook his head.

They turn to enter the room Eggman designated for Shadow quite literally this morning actually, it may only have a bed at the corner but it was miles better than the guarded room he woke up in– full of pipes and beeping buttons deep underground, not to mention that Omega-robot residing there.

He may be the ultimate life-form but after a tussle like that, even he needed to sit down. He slightly sinks into the mattress, letting him feel inclined to release a heavy sigh, his mistake. “Guh–” He winces, closing his mouth when his jaw throbbed just for breathing wrong.
Mildly annoyed, Shadow crossed his arms while facing Eggman, a tight grip to the brown scarf still in his hands.

 

Possibly trying to undermine his bad calculations, “No matter, we know your current state thanks to the fight,” Eggman brings up the good the stalling had done. To his credit, Shadow did assess his abilities during his brawl with the blue hedgehog, coming to a disappointing conclusion of his own skills which is; Not good enough.
Fortunately, “AND I’ve got the chaos emerald you can use for MORE power!” Eggman did something right tonight. He pulls out a white chaos emerald which exudes raw chaos-energy that allowed Shadow to feel some sort of ease ever since he was first woken up from his long slumber.

Wordlessly, he accepts the chaos emerald and closes his eyes– encased by the tingling sensation of chaos energy running through his body, the discomfort from earlier eventually phasing out. Minus the sore muscles and high temperature due to his first fight in technically– YEARS.

It had been… thrilling, to say the least. Fascinating that an ordinary mobian could have been so fast and begrudgingly skilled. He had also been amusing– displaying a unique fighting style resembling a sort of dance and spouting nonsense Shadow never thought to hear during a fight as intense as the one they had, none of his targets ever had the chance to utter a word when faced with him.
He supposed it’s something only a mobian could be capable of after all, except the (very vague) ‘mobian-101’ classes he took back in the ARK did not prepare him for that sort of encounter. Or warn him that the smell of a mobian could be so…

Shadow grimaced, confused on why despite the chaos emerald clearly working– his body still felt uncomfortably warm.

Shadow stares at Eggman for answers who had been watching him while taking notes on a tablet presumably about him. It reminds him of the researchers and scientists behind glass. Their gazes meet only for a moment but that is enough for Eggman to immediately hide his hands behind his back, flashing him a clearly forced grin of innocence.

Putting the chaos emerald into his mass of quills, “...What is he?” Shadow focused his sight on the brown-scarf in his hand– giving it a frustrated squeeze as he recalls that infuriating smirk and voice of the garment’s owner.

“Sonic?” Eggman tilts his head to the side, “Clearly he’s a hedgehog such as yourself–err… sort of.”

“No you idi…” Shadow cuts himself off, rubbing the bridge of his nose, mustering all of his will to remain remotely respectful. “His secondary-gender.”

“Oh–?” Clearly, his question came out of the blue. “Sonic is an omega and apparently looking for a mate and failing horribly according to village gossip. Not– Not that I! That I listen in, ahem,” Fortunately Eggman gives a coherent (enough) answer, revealing a few things he didn’t plan to but Shadow could care less about the eccentric doctor’s past-times. More importantly– he was mostly in shock.
After all, other than the (enticing) fragrant scent that caused him to be here in the first place– Sonic is far from the omega-stereotype he’s learned about; dainty, fragile, submissive… so basically, the opposite of what Shadow faced.

“It doesn’t even matter, his entire-being is a nuisance!!” Eggman blabbered lightly about the topic at hand. Clearly ignorant of what Shadow had to deal with.

It's only when Shadow doesn’t reply to agree that they stare at each other in silence.

That seemed to be all Eggman needed to piece two and two together. “Wait…“

Eggman pinches his chin, a thoughtful look on his face, actually looking like a respectable doctor for once. “I suppose your first meeting with a mobian would obviously have unexpected repercussions with pheromones and all…” He muttered, sounding amused. Only now considering the fact that Shadow never had mobian-contact until tonight and would you look at where that led? Shadow incapacitated.

Bothered by such a weakness, Shadow merely replies with a soft grunt, struggling to even accept the fact. Out of everything– it’s the scent of some random mobian that had him on his knees? Not even from their fierce fight? Ridiculous.

“Now for a solution! It’ll take me a week or so to make pills that make you resistant to pheromones due to your alien biology so for the meantime…” Eggman clasps his hands together, a crisp ‘slap’ startling Shadow out of his thoughts. “Exposing you to other mobians should be a start but to who…” Personally, Shadow would rather avoid ‘socializing’ but he knows better than anyone that he doesn’t have a choice.
He tugs the collar around his neck to no avail like many times before, a blatant reminder.

“Perhaps I can kidnap– borrow a pushover mobian somewhere to do the jo–”

The door slides open, startling both Shadow and Eggman.

“Um sir–” Orbot– the circle-head red robot meekly peeked inside, hands holding the frame of the automatic doors.

Seeing as it was nothing ‘important’, Eggman scoffed, “Not now Cubot! Continue cleaning the vents,” immediately dismissing the robot away.

“About that sir–”

“THERE’S A GIANT WINGED-RAT IN THE VENTS!” Cubot’s voice sounded grating to everyone’s ears involved even when Orbot tried to shut him up by pushing him away, the yellow-bot persisted in flailing his arms in the air.

“WHAT!?” Roared Eggman, giving Shadow another reason to cover his ears in disdain.

“Shadow– stay, recover,” Eggman turned to him, giving direct orders as if Shadow had any other plans he could do.
When Eggman receives a dull nod, he runs to the two minion-bots ”Hurry you idiots! Take me there!” the two robots scurrying off as Eggman followed— his angered stomps echoing around the small room until the door shuts closed.

He stared at where Eggman once stood, finding the lack of company ever since his awakening… unsettling.

With no rambling or orders from Eggman to distract him from his mind, the silence becomes unbearably loud to his ears. Forced to hear his own slow breathing and the heavy thumps of his still beating heart, reminding him that despite it all– he is still alive.
Now under the control of Doctor Gerald’s descendant.
Back in another empty white room with only a bed.
Once more tasked to fight for reasons he could care less.
Still alive and without Maria.

He looks up at the ceiling, falling to the bed on his back despite how his rigid-quills get in the way– the sickening color of pure bright white making it near impossible to relax. The smell matched the color, unnaturally clean and bitter, sterile, in other words. The opposite of mobius; rich and diverse.
It first overwhelmed him but he found himself craving for all the other unique sensations that came his way as he followed Eggman for the chaos emerald.

Closing his eyes with a heavy sigh, he recalls the smell of nature that matched with every image in the books he read with Maria– a feat he never thought to be possible.
Yet he smelt it. The fresh air was nearly overpowered by the sharp scent of grass, herbal smells from towering trees, shrubs that tickled his nose and beautiful flowers that smelt like nature’s perfume, calling for him to see what else he can experience now that he is no longer in space.

Maria would probably like the smell of the air and wind… it’s different from the one they were used to, far too stale to the point it could only be described as nothing, purely meant for them to breathe and live; a necessity.

He likes the smell of the wind.

His eyes open to look at the brown scarf on his hand, taunting him motionlessly.

Sonic smelt like the wind itself. Seemingly a whisper of everywhere he’s been all at once.
It wasn’t obvious at first, only when he tugged at the scarf was he hit by a calming fragrance that overwhelmed him with… feelings?? A foreign sense of smug and anxiety he’s certain is from Sonic– itching a part of him that he didn’t think was ever there, harshly calling out the unnecessary side of him that was designed to be an ‘alpha’.
A need and desire he didn’t understand, this– gravitational pull yelling at him to–!

The memory makes him click his tongue in protest, throwing the darned scarf to the wall which slid down to his bed.
He covered his nose– aware of the only organic lingering scent that called for him in this small room.

He stared, feeling mocked.

Does that stop him from grabbing it back anyway?

…No.