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What He Didn't See

Summary:

After two years of silence, Shepard finds herself caught between Cerberus orders, Miranda’s scrutiny, and her own doubts. But nothing tests her resolve more than Horizon — and the ghosts it awakens.

Chapter 1: Wake up

Chapter Text

Was it all really happening? Just minutes after waking from a two-year coma, was she supposed to hunt down killer robots bent on her destruction? The universe felt suddenly unreal. Like a fever dream, she couldn’t wake from. The last thing she remembered was the Normandy’s explosion, drifting in the void, suffocating in the cold black silence of space. And yet here she was, alive, standing on a brand-new ship. A Cerberus ship.

Cerberus.

The word alone twisted her gut. They had broken into the deepest secrets of the old Normandy, built a bigger, shinier replacement in secret and now they wanted her to command it, draped in their colours. Her first reaction was revulsion. She hated Cerberus. Their ruthless, dangerous ideology clashed violently with everything she stood for. And yet they were the only ones who had actually acted against the Collectors. The Alliance? Idle. The Council? Useless. They owed her nothing. They never had.

The moment she stepped onto the Normandy SR-2, a strange mixture of awe and unease washed over her. She hadn’t expected the new ship to be a carbon copy of the old one. Cerberus certainly knew how to build a ship. But the polished steel, the clean lines, and the subtle hum beneath her feet felt alien. And then there was the AI.

Memories flickered unbidden. Two years ago, a rogue AI had turned against her team. The last thing the machine had said before shutdown was… Help. The echo of that message haunted her still.

“And? What do you think of the ship?” Joker’s voice broke through her thoughts. The pilot was perched in his seat, grinning like a kid with a new toy. “Leather seats. Comfy as hell. Cerberus knows quality way better than the Alliance ever did.”

“She’s impressive. Must’ve cost a fortune,” Shepard murmured, eyes drifting to the stars outside the cockpit window, an endless, beautiful universe stretching beyond.

“Not more than your reconstruction.” Joker smirked but fell silent when he caught her pained expression. The scars on her face told their own story — scars from being pulled back too soon, from the agony she tried to hide. He didn’t want to ask how she was feeling. Jules wasn’t talking either. Too many ears onboard. The AI was always listening, logging, reporting for Cerberus.

“Actually, I wonder…” Shepard’s voice was soft, almost fragile. “Why spend billions on me? I’m just a person.”

“You stopped Saren. Prevented a Reaper invasion.”

“That wasn’t me alone. I had a team.”

“You led us.” Joker’s smile faded. He changed the subject. “Have you seen your cabin yet?”

“No.”

“Then what are you waiting for?”

“I… don’t know. It’s all just…”

“Strange? You’ll get used to it. Promise.” Joker winked and nudged her out of the cockpit.

The lift ride up was silent. The AI tried to engage her, but Shepard ignored it. Not out of spite, more from nervousness. The ascent felt endless. Every passing second brought a tightening in her chest. She couldn’t shake the feeling that the ship might explode at any moment.

When the doors slid open, a second set of doors revealed her cabin. She stepped inside and the uneasy feeling deepened. The space was larger than expected — more spacious than anywhere she’d lived in years. Why so many privileges? A private bath, an aquarium with shimmering fish, a large window in the ceiling offering a breathtaking view of the stars.

She wanted to be angry. She wanted to reject all of it. But instead, something dark welled up inside her. A sudden tightness in her throat, a rush of heat through her veins. Her breath hitched. Her hands trembled.

No.

Not here. Not now.

The stars outside blurred, spinning faster, faster. She dropped to her knees, clutching at the bed frame as her heart pounded against her ribcage like a drum. The room felt too small, too loud. The ceiling window above became a black vortex swallowing her whole.

Suddenly, she was back on the Normandy SR-1.

The alarms blared. Red lights pulsed violently, the ship shaking from the explosion. She could hear Joker’s desperate voice over the comms, her crew shouting orders, panicked. Smoke choked the corridors.

She gasped for air that wasn’t there.

The void.

Cold.

Silent.

Dark.

The last thing she saw was the burning wreckage of the Normandy drifting away, and then…

She was here.

 

The panic attack consumed her. Sweat beaded on her forehead. She felt trapped inside her own body, unable to control the rising tide of fear. Her mind screamed at her to run, to fight, to wake up from this nightmare.

Slowly, she forced herself to breathe. In through the nose, out through the mouth.

Inhale.

Exhale.

The stars outside her ceiling window were still there. Quiet. Vast. Real.

She was alive.

But at what cost?

After several minutes, the tightness in her chest loosened. Her fingers stopped trembling. Shepard slumped against the bed, breathing shallow, heartbeat still erratic. The silence of her cabin pressed in, oppressive.

She couldn’t tell if the calm was relief or emptiness.

Memories flooded back. Faces of friends and allies lost. The weight of command. The endless struggle against impossible odds.

Why was she alive when so many others had died?

Was this second chance a gift or a sentence?

She looked at the ceiling window again. The stars burned cold, distant. Like witnesses watching her falter.

She touched the scarred side of her face, a physical reminder of her near-death and forced resurrection. A souvenir of survival and pain.

Somewhere deep inside, a stubborn flame flickered, determination. The same fire that had led her through countless battles. She would make this second chance count.

She would lead. Protect. Fight. Whoever took those poor colonists will see hell.

 

Later, Joker came by her cabin door, asking gently for permission to enter.

“Hey, are you okay?” His voice was softer now, lacking the usual cocky edge as he entered.

Shepard wiped her eyes, trying to compose herself.

“Yeah,” she said quietly. “Just… adjusting.”

He nodded, understanding more than words. The second he had entered her cabin, he could feel that something had happened. Aside, EDI’s note that he should check on Shepard.

“You don’t have to pretend here,” he said. “We all carry scars, seen and unseen.”

She wanted to believe him.

Maybe, on this ship, she wasn’t alone.