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English
Series:
Part 2 of It's a Long Road Home
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Published:
2025-12-03
Updated:
2026-04-12
Words:
46,738
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16/?
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85
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The Long Shadows of Yesterday

Summary:

After eight years apart, Peter finally came home. He finally had a family again. One that loved him, fought for him, and made the world feel safe in a way it never had before. But the thing about happiness is that it only lasts for so long. Especially when there are people who believe Peter isn’t anything more than a project that slipped through their fingers.

When Hydra and Oscorp strike, Peter is taken once more, isolated and tricked into believing Harley was killed after Peter disobeyed. Tony is fed the same lie about Peter to shake him off their tail, shattering the fragile healing they’d only just begun. With both sides grieving ghosts that are still alive, enemies tighten their hold, convinced that Peter’s powers and his pain belong to them.

Locked away in a place built to break him, Peter fights to hold onto himself as the people who love him try to bring him home again. Old trauma resurfaces, new threats close in, and every moment lost to manipulation pushes them closer to a truth none of them are okay with.
A sequel to The Echoes of These Long Years
*Updates every Saturday*

Notes:

(See the end of the work for notes.)

Chapter 1: Unraveled

Chapter Text

Dinner in the Stark penthouse was loud in the easy, familiar way it always was, with everyone talking over each other while pretending they weren’t. Pepper set the pasta bowl down and immediately had to redirect Harley’s wandering hands. “Use the serving spoon,” she warned, pointing at him like she’d been waiting all week to do it. “I am using it,” Harley argued, even though he very clearly wasn’t. 

Tony slid a piece of garlic bread off Morgan’s plate, only for her to shriek, “Dad! That’s mine! Get your own, there's a whole plate over there!,” while Peter tried not to laugh so hard that he inhaled his water. MJ shook her head at the whole scene, muttering, “This feels like a zoo on visiting day,” and Ned recorded it like he was filming a nature documentary. It was messy and loud and warm, and Peter still had moments where he couldn’t believe he got to sit in the middle of it.

Halfway through dessert, Harley froze mid-bite like he’d just been hit with divine inspiration. “Oh my god. Arcade night,” he declared dramatically, knocking his fork onto Ned’s lap. “We haven’t been in, like, forever. And I need to reclaim my air-hockey crown.” Ned nearly choked on his soda. “Reclaim? You only won because the puck got stuck in that weird corner and you pretended it was a skill issue on my part.” Harley waved this off. “If the puck feared my power, that’s not my problem.” 

MJ raised an eyebrow and said, “You’re the only person I know who can talk trash about an inanimate object,” and Harley immediately bowed like she’d given him a compliment. Peter laughed under his breath, feeling something soft settle in his chest; this was exactly the kind of night he used to dream about when he was little.

Before Peter could voice an opinion, Morgan gasped loudly enough to interrupt everyone. “Can I come too? Please? Pleasepleasepleaaaase?” she begged, leaning halfway across the table like a tiny lawyer arguing her case. Pepper didn’t even look up right away. She just stared at her plate, gathering strength. 

“If you guys can watch her responsibly,” she finally said, making sure to look directly at Harley, “then yes. But you need to be back by ten. Ten. Not ten-oh-five. Ten. And no negotiating, that’s being generous. Already past Morgan’s bedtime.” Morgan slammed both fists onto the table in triumph. “Peter, you have to help me beat the claw machine again!” she said, bouncing. “I won the octopus last time.” Harley groaned. “Yeah, and then you cried because it had ‘too many legs,’ remember?” Morgan instantly crossed her arms. “It was suspicious-looking! I stand by that!”

When Tony asked, “All right, so which one of you is officially in charge tonight?”, Harley, MJ, Ned, and Morgan all pointed at Peter like they’d rehearsed it beforehand. Peter nearly dropped his fork. “Why me?” he demanded. “Harley’s older!” Harley pressed a hand over his heart dramatically. “Peter, I’m far too creative and impulsive to be responsible for- ” He gestured vaguely toward Morgan and Ned, who squinted at him like they weren’t sure they liked being described as a hazard. MJ pushed her plate forward and said, “Peter’s the only one here who won’t accidentally set something on fire.” Ned nodded solemnly. “He’s also the only one of the two who didn’t lose their shoes last week.” Harley groaned. “OH MY GOD, I lost them one time!” Tony rested a hand on Peter’s shoulder. “Congratulations, kid. You’ve been unanimously elected team supervisor.” Peter gave him a betrayed look. “You should be protecting me.” Tony only grinned. “Yeah, but watching you suffer is funny.”

The getting-ready process was absolute chaos in the way only Stark-family outings could be. In the hallway, Morgan insisted she needed her light-up sneakers because, “They make me faster and stronger, duh,” and MJ helped her get them on while Harley accused Ned of hiding his jacket. Ned held up both hands. “Why would I hide your jacket? I’m literally wearing a T-shirt with Star Wars on it. I don’t need accessories.” Harley snapped his fingers like he’d solved a mystery. “Morgan hid it.” She gasped, offended. “I’m ten, Harley! I don’t do that anymore.” Peter tugged on his own shoes while watching the scene unfold with a mix of amusement and affection. Tony handed Harley a fivety as sneakily as a man in an action movie passing intel. Pepper sighed from the kitchen doorway. “Tony, please tell me you’re not funding candy.” Tony smiled innocently. “Of course not.”

“It’s totally for candy,”  Harley whispered, and Peter shoved his shoulder.

Morgan grabbed Peter’s hand as they all walked toward the elevator. Before the doors fully closed, Tony called out, “Ten o’clock!” Pepper added, “And no letting Harley trick anyone into eating anything questionable.” Harley gasped like he was offended by the truth. MJ called back, “No promises!” Peter gave Tony a half-smile, the kind he didn’t even realize he’d started doing until a few months ago. Tony’s expression softened into one of those quiet, proud looks that always made Peter feel steadier than he knew how to explain. “We’ll be back by then, promise.” Peter promised. Tony nodded. “Have fun.”

Inside the elevator, the sound bounced around the walls, Morgan humming, Harley talking about air hockey like he was entering a championship, Ned explaining his strategy, MJ roasting half the group just for existing, and Peter smiling at all of it. It was warm in a way that wasn’t loud or forced or temporary. It settled into Peter’s chest and stayed there. This was home. This was his family. And heading to an arcade on a Friday night felt like exactly the sort of simple, normal happiness he’d once thought he’d never have.

  -

Someone from the Tower’s security staff ended up driving them that night, since Happy was out of town for a conference and Tony didn’t want his kids walking out in the cold. It wasn’t a long ride, maybe ten minutes at most, but it gave Morgan exactly enough time to alternate between leaning over MJ to point out random storefronts and listing every game she planned to beat at the arcade. Peter watched her with this soft amusement, like he still couldn’t quite believe how much energy a ten-year-old could store in such a small body. Harley made jokes from the middle seat, kicking Peter’s foot every few minutes just to be annoying, while Ned narrated everything happening outside the window, still filming his documentary. By the time the car rolled to a stop, the night already felt bright and easy in that way weekends sometimes did when everyone was in a good mood.

The moment they stepped out into the glow of the arcade’s neon sign, Morgan bolted ahead, only to be caught by the hood of her jacket as MJ hooked a finger into it. MJ laughed, steadying her. “Slow down, speed demon. We haven’t even gone inside yet.” Morgan just grinned up at her, bouncing on her toes, as if physically incapable of standing still for more than half a second. MJ squeezed her hand, adding, “By the way, I’m borrowing her tonight. I’ve always wanted a little sister.” Morgan gasped dramatically and shouted over her shoulder, “Peter, she’s adopting me!” Peter groaned, running a hand through his hair. “That’s not how adopting works.” Harley slung an arm over Peter’s shoulders, smirking. “You'd better fix that, man. You’re losing custody fast.”

Inside, the arcade swallowed them in a rush of sound and color, ringing bells, digital chimes, and bright flashing displays lining every wall. MJ and Morgan drifted off almost immediately toward a climbing structure, Morgan dragging her with the determination of a tiny general leading her chosen soldier into battle. The boys claimed the air hockey table, because that was tradition, and Ned was already feeding quarters into the slot before anyone else could suggest a different game. Peter scored the first point in three seconds, and Harley’s jaw dropped in outrage. “Nope. Absolutely not. You cheated.” Peter only lifted his brows, trying not to smile. “Harls, it’s literally just air hockey.” Harley jabbed a finger at him. “You have spider-reflexes. That is cheating.” Ned snorted, leaning on his mallet. “My guy, you’re only mad because you’re losing.” Harley pointed at the scoreboard like it had personally betrayed him. “This is a warm-up round.”

The game went on with the exact chaos expected of three teenage boys who took dumb competitions very seriously. Peter’s movements were smooth and quick, and Harley continued narrating every difference in reaction time like he was building a legal case. Ned kept switching sides, cheering for whoever wasn’t currently yelling at him, until Peter finally tapped the puck in for the winning point. Harley threw both hands in the air as if appealing to a higher power. “Rigged! Completely rigged. I want a rematch when he’s asleep.” Peter laughed, shaking his head. “That’s… not how I work.” Harley huffed. “Well, maybe it should be.” Ned grinned at them both. “You know Tony would totally install a power button if he could.” Peter groaned. “Don’t give him ideas.”

They wandered to the little café tucked into the corner of the arcade once the fun ended, still bickering lightly the whole way. It was small but warm, filled with mismatched chairs and the smell of fryer oil and melted cheese. Morgan and MJ had already claimed a table, Morgan proudly guarding a stack of prize tickets that was bigger than her head. MJ gestured at them with the air of someone announcing breaking news. “She’s a prodigy. She obliterated the basketball game. I’m pretty sure the machine short-circuited out of shame.” Morgan puffed out her chest. “I got ninety-two!” Peter slid into the seat beside her and ruffled her hair. “Look at you, Mo. You’re gonna bankrupt this place.” She beamed and nudged the giant pile of tickets toward him. “You can have half. But not all. I need the giant frog.”

Harley leaned back in his chair, smirking. “That frog is mine, actually. I’ve already bonded with it.” Morgan gasped, scandalized. “No! He’s my frog!” MJ patted her shoulder. “Don’t worry. Harley can visit the frog on weekends.” Ned broke into laughter so abruptly he nearly spilled his milkshake. Peter rolled his eyes, still smiling. “You’re all so dramatic.” And yet the table felt warm and safe, full of overlapping conversations and friendly teasing. They shared nachos, mozzarella sticks, and way too many milkshakes, talking over each other the way people did when they were entirely comfortable. MJ teased Peter for “air hockey showboating,” Harley reenacted the “cheating scandal” with increasing exaggeration, and Ned launched into an excited explanation about the new robotics project he and Peter were planning.

It was loud and cozy and familiar, the kind of night that didn’t feel special on the surface but would stick with them anyway. Peter leaned back in his seat at one point, looking around at the laughter, the soft glow of the café lights, Morgan swinging her legs under the table, and felt that rare sense of peace settle over him. Things were good. Really good. And sometimes, that was enough to make a moment feel perfect.

  -

Peter’s spider sense tingled. He looked around. The café was quiet around them, the bored girl behind the counter barely glanced up as they joked, the kind of casual laughter that usually settled in like a warm blanket. But Peter couldn’t shake the cold prickle crawling up his spine. When six men in grimy construction gear walked through the door, dragging dust and exhaustion with them, something deep in his chest clenched tight.

They looked like they’d been working a brutal, endless shift, faces set in tired lines, eyes sharp and calculating. Peter’s skin crawled, every instinct screaming, but he forced a smile and stepped out of their way, trying to drown out the warning bell ringing in his head.

He tried to focus on the easy back-and-forth with Ned, but his thoughts wouldn’t settle. The pit in his stomach twisted into knots.

Then Harley’s voice sliced through the room, sharp and tense. Peter looked up. His unease ballooned into cold panic, nausea curling at the back of his throat. He needed air, needed space.

He moved toward the counter, ordering water with a voice that sounded distant, like it belonged to someone else.

And then everything exploded.

Kyle, the man Dad had sent to watch over them, collapsed like a rag doll. Blood bloomed dark and fast, seeping through his suit right over his heart. Peter’s stomach lurched violently. His breath hitched, chest tightening as the world tipped sideways for a moment.

But there was no time to fall apart.

Three men grabbed MJ, Ned, and Harley, holding them tight, their grips unyielding and merciless. A fourth had Morgan, small and trembling in his arms, pressed tight against his chest. The knife gleamed cruelly, cold steel hovering over her tiny shirt, pressed right against her chest.

Peter’s body moved before his mind could catch up. He lunged, desperate, reckless.

A fish-like hand clamped down on his shoulders, wrenching him backward. Pain flared as a taser struck his ribs, fire exploding through his body. His legs buckled, knees hitting the floor.

His arms were forced behind his back, bound cruelly. Panic blazed in his chest as he looked around. Ned and MJ were pinned to the wall, hands forced behind them, eyes wide but fierce. Guns glinted in the hands of their captors.

Harley was on the ground, a knee dug hard into his spine. Every struggle was met with violence; an elbow to the back of the head silenced his protests.

“Stop moving!” Peter shouted desperately. Harley’s eyes met his, wide with pain, and then he stilled, swallowing a groan.

Morgan’s terrified cry shattered the chaos, piercing straight through Peter’s heart. He turned toward her, pain and fury roiling in his gut, ready to fight for her with everything.

And then the taser hit him again, harder this time. The world spun wildly as he collapsed forward onto his knees, breathing raggedly.

A cold, sharp prick in his neck told him that something had been injected into him. The vile syringe dropped to the floor with a careless clatter.

“We know you’re Spider-Man,” a voice rasped, and Peter’s blood froze. No. This was why they were here. Because of him. Because of who he was. They were hurting the people he loved to get to him.

“What do you want?” His voice cracked, half despiration, half defiance.

“For you to come with us,” the largest man said, voice low and unkind.

Peter’s eyes flickered between them, MJ’s jaw clenched tight, Ned’s glare fierce despite his bound hands, Harley’s pale face twisted in pain, Morgan’s small sobs heart-wrenching in the cold air.

He nodded, barely able to trust his own shaking hands.

“You’ll let them go?” Peter’s voice was desperate, a plea.

MJ’s sudden protests to his words were cut off with a brutal slam of a gun butt striking the back of her head, not enough to seriously injure, but enough to silence her.

“Yeah. Your friends go after the hour. We need time.” The man’s words were cold and final.

Peter swallowed the dread rising in his throat.

Harley started to speak but was silenced with a cruel dig of the knee into his spine, his voice breaking into a strangled cry.

The man holding Peter yanked him up by the hair, pain flaring through his scalp.

Weak and trembling, Peter stumbled after them, every step a battle against the drug coursing through his veins, draining his strength. He was broken and beaten, but not defeated. Not yet.

The car door slammed shut behind him after they bound his hand to the handle on the car ceiling, trapping him in darkness.

The engine’s hum was both a lullaby and a warning.

Everything was blurring in and out.

His head lolled sideways, resting on his bound arm as the shadows closed in.

And then… nothing.