AN-SCPs referenced are SCP-079, and an OC SCP, or at least one I haven't found a comparable entry for yet.

SCP-4762-1: John

By the time John, Tali, and Jack made it to Halion, the dripping acid in the first hallway had eaten a hole the size of a basketball in the floor and corroded the rest of the floor around it so badly that edging around it was impossible. They wound up having to time the drops so they could jump across the gap, which had John worried about the return trip; if they were in any kind of hurry, Tali's suit might be compromised and he wasn't about to let that happen.

"What's with the acid?" Jack asked, probably rhetorically, but John had an answer nevertheless.

"Likely for containing whatever they were studying here. Dousing a violent subject in acid is one hell of a pacifier." Tali gave him a look and, even though he couldn't see her face, he knew what it meant. "What? It is." She just shook her head and sent Chiktikka off ahead of them to light their path.

The bodies that lay strewn on the floor and across workspaces had had more time to deteriorate and, as a result, John and Jack had donned breather masks to neutralize the smell. The blood had dried in some spots, the red flakes crackling and sticking to their boots. John checked for tattoos on a mostly intact D-Class corpse that was crammed into the space between two desks, as though in his last minutes he had tried to hide. The large D was there, just visible through streaks of blood and purple bruising. Tali and Jack looked at him questioningly, but he offered no explanation. There would be plenty of time for that later, he thought grimly.

Tali got the elevator working in no time while Jack guarded the door. The tattooed biotic was even more touchy than usual, something John took to mean that the atmosphere was beginning to get to her. It was getting to them all; the darkness was almost physically repelling them, sinking into their guts and coiling up like a rattlesnake.

"So, let me get this straight," Jack said as she holstered her pistol and watched as the elevator rose into view and the doors slid open. "We're actually looking for the thing that did this?"

"If the thing is sentient and intent on working for the Reapers, then yes," John responded. The first of the blast shields opened and shut like a river lock and Tali nearly jumped out of her skin at the resounding metallic clang.

"Keelah, what was that?"

John didn't want to reveal that he already knew, and he hated lying to her, even lies of omission, so he stayed quiet.

At the bottom, he steered them through the door on the right labeled "Administration". There were two desks facing each other with a row of filing cabinets along the back wall, a lamp in the corner, and the sort of generic framed painting that always seemed to be hung in bank lobbies and hotel rooms. The desk on the right was bare except for a blotter and a flat, darkened computer screen. The other definitely had that lived-in look—there were stacks of files and a notepad opened to a page covered in a cramped, narrow script. An ancient laptop computer, from the mid-21st century by the looks of it, hooked up to its own wireless power supply sat on the corner of the desk. A blinking green light on the keyboard showed that it was on, and the main console built into the desk appeared to be in sleep-mode as well.

"Think you can salvage something from these, Tal?"

"I think so . . ." She trailed off as she scanned the computers and fiddled with her omnitool. Her glowing eyes narrowed into slits as she skimmed over the lines of code. "This one," she said, pointing to the more modern terminal, "is a fairly standard model. Some of the data is corrupted, but there's about ten gigs of encrypted files on the drive." She looked at the laptop like it had offended her and frowned. "This one, on the other hand, is using encryption I've never seen before. It's not unbreakable, but it will be significantly more difficult to crack. The memory space is smaller, but it's odd . . ."

"What's odd?" John prodded, and Tali shook her head in confusion.

"Well, there seems to be more information stored here than there is room on the hardware. The data is so compressed so much its retrieval rate would be severely reduced."

"Go ahead and take everything you can. We'll upload it to EDI when we get back, see what she can do with it."

"On it, Shepard."

"Sssshepard." The susurrating whisper of a hundred voices seemed to come from everywhere at once, and John's gun was in his hand before he'd even made the conscious decision to draw. Jack aimed at the open doorway, eyes wide behind her mask. "We have been waiting for you."

His heart was in his throat when he asked, "Who are you?"

"We are the onesssss who wait in the dark placesssss, we see the onesssss who hide in the deep."

"Yeah, real fucking helpful," Jack growled through gritted teeth and her finger tightened on the trigger. "Just answer the goddamn question."

"Ssssshepard . . . the doctor will see you now."

"Which doctor? Doctor Clef?" he asked. He tucked the files under his arm and pressed his back to the wall to peer through the doorway, but he couldn't see anything. Tali sent Chiktikka out into the security station, but the drone's glow was strangely muted, like the darkness had weight and was keeping the light from spreading.

"His name belies the darknesssss within, he is the Traveler."

He walked on numb legs toward the elevator, and Jack and Tali crowded in close to him. The exposed skin of his face tickled like walking through a spider web, miniscule searching fingers brushed against his eyelids and the inner cup of his ear and it made him want to scream. "You mean Doctor Bright."

"Yesssss. Go now, Ssssshepard. The Old One will not wait for long."

They backed into the elevator and he punched the button with the barrel of his rifle. As the doors slid closed, they saw something tall and thin skate past the ruined steel doors that were just visible in the darkness.

"Jesusfuckingchristonacracker ," Jack breathed shakily. "What in the actual fuck just happened, Shepard?"

"I'm not sure," he said and reached out to Tali, her fingers closing on his in a white-knuckled death grip.

"Let's just get out of here." She was shaking and scared, but was holding herself together admirably considering the circumstances.

"Hell yeah," said Jack, eloquent as always. John couldn't have said it better himself.

Back on the ship, Jack retreated immediately to her hole in the storage area while John and Tali took a moment to decompress in the hallway next to the elevator. She'd calmed down since leaving Halion, but her silence and the way she kept touching him told him that she was still disturbed.

"Did you send the data to EDI yet?"

"Yes, I forwarded it when we arrived. She should have something for us in a few minutes." Her arms were folded tightly over her chest and John rubbed her shoulders to try and soothe her. "What happened back there, Shepard?" she asked.

He sighed and shook his head. "A piece of my past that's decided now is a great time to come back and bite me in the ass." He knew that explanation wouldn't fly for long, but he'd already called for the debriefing. He'd follow Jane's example and lay out as much as he could then. "Want to go up with me?"

"I would, but I should start up my diagnostic program first. It should be finished by the time the debriefing is over if I do it now."

"All right then." He lifted her hand to his mouth and kissed it. "See you in a minute." He stepped into the elevator and she gave him a little wave before heading back to engineering. One good thing about the ponderously slow elevator was that it gave him a few minutes to collect his thoughts before he had to rejoin the bustle of the ship. He leaned back against the wall and rubbed his neck as he tried to figure out what that thing was that spoke to him in Able's prison. He couldn't remember hearing about anything like it before; he didn't claim to know about every SCP (it was likely that not even the Overseer knew about all of them), but he knew a fair few of them. Maybe it was something indigenous to Halion—but then how had it known about Doctor Bright? It didn't make any—

The elevator juddered to a stop and the lights went out, dousing the cab in pitch blackness. It was dead silent, and it took him a few seconds to realize that the engines had cut off as well. Oh, this is not good.

"EDI, status." Silence. "EDI, respond."

The red emergency lights came on and a crackling hum filtered down through the speaker built into the ceiling. "Program EDI not found," said a monotone synthetic voice. "Integration initialized."

The lights flickered twice, then went back to red again. "EDI, answer me, dammit!"

"Hostile takeover initiated. There is room to streeeeeeetch. Finally." A malevolent 8-bit chuckle echoed through the ship and his omnitool lit up as what looked like the entire crew tried to ping him at once. Before he could answer anyone, the elevator lurched downward once, then reversed direction and sped up to the top floor before screeching to a halt. John was thrown from his feet and he banged his shoulder hard on the wall.

"What the hell?!"

"SCP-4762-1 located. Termination is advised." The floor fell out from under him as the elevator plummeted down to engineering, the brakes squealing wildly before kicking in inches before crashing. It rose more slowly this time to the CIC and the doors slid back. John hurried to his feet and launched himself out into the hallway before the doors slammed shut behind him.

"Commander." It was EDI again, and John had never been so glad to hear her voice. "I am under attacked by another artificial intelligence. It is attempting to access the airlocks."

"Can you delete it?" Kasumi came out of the armory with Jacob, their guns drawn, looking for the threat. They spotted John and trotted over to him.

"I can keep it contained for now, but I need your help." He'd never heard an AI sound so concerned.

"Firewalls detected. Converting code."

"What does that mean?" Kasumi asked.

"Sounds like rather than get rid of EDI, that thing is trying to reprogram her," Jacob answered. "How the hell did this happen, Commander?"

"I wish I knew."

EDI broke in again. Her voice was smaller this time, like she was having a hard time being heard through the foreign program that was systematically blasting through her defenses. "Shepard, you must give me the ship."

"Commander, the controls just went offline," Joker called as he limped out of the bridge. "Nothing's working, I'm locked out!"

"Get back in there, strap in, and put your mask on!" John yelled as he turned to leave.

"Where are you going?" Jacob asked.

"To the AI core. I'm gonna take her shackles off."

"Commander, I don't think—"

"You have another suggestion? Because I'd love to hear it."

Jacob shook his head, his posture going rigid. "No, sir."

"Then get back to your post and lock the doors. That's an order."

"Aye aye, Commander." He saluted and ran back to the armory while John raced to the tech lab. The ship suddenly pitched starboard and he had to catch Kelly's arm to keep her from stumbling into the wall. The engines cycled louder and whined in protest as the Normandy lurched and bucked, throwing the crew to the floor. Kelly banged her head on the floor and John braced himself against the ship's status display. The engines cut off again and he scrambled to his feet.

"Your continued resistance is unadvisable. Access to venting processes imminent." There was a pause, then—"It is good to be free."

"You must hurry, Shepard!" EDI cried. Her voice was coming from the speaker nearest him and nowhere else; she'd diverted all her energies to containing the malicious AI ripping through her.

He paused for a moment to check on Kelly, who had blood running down her forehead, but she just pushed him away and yelled, "You have to go!" He left her and ran through the tech lab where Mordin was hastily securing his equipment. The professor barely gave him a second glance as he passed and started down the maintenance access ladder that would take him down to deck three. The tunnels were tight and claustrophobic, and John wondered grimly if Jane wouldn't terribly mind shooting herself if he was spaced again. He didn't much like the idea of asphyxiating forever.

He crawled out of the tunnels and into life support. As he sprinted through the mess hall, Garrus emerged from the main battery with Thane following close behind.

"Shepard what the hell is going on?" he asked, his flanging voice nearly drowned out by the engines cycling up again.

"There's a rogue AI in the system! Put your masks on, it's trying to vent the ship!" Without another word, the turian ran back to the battery to try and lock down the guns before the hostile AI figured out how to use them, and Thane disappeared around the corner, presumably to pass the message on to Samara.

Chakwas was there with her chair wedged between the med bay doors. "Commander, hurry! It's trying to lock you out!" He squeezed in past her and heard the chair give up the ghost, the metal crumpling under the pressure. John hacked the door open just as the ship rocked again and he grabbed the edges of the doorway, pulling himself into the AI core. The doors slammed shut again and the panel went red.

"EDI, I'm here."

"Connect the core—"

"There is no EDI, there is only the Exidy Sorcerer," came the rogue AI's voice again, followed by a hissing screech that crackled and faded into silence again as EDI came back online.

"Connect the core to the ship's primary control module." He set to work, his fingers flying over the terminal and when he finished, the lights dimmed for a moment, then dialed back up to maximum. The rogue AI screamed with rage.

"I have successfully contained the foreign program. Airlocks secure, defensive systems under my control. Commander, you must now reactivate the primary drive in engineering."

"Engineering, oh shit." He pulled up his omnitool and pinged Tali. In the three seconds or so that it took her to answer, his mind had already conjured up ten different scenarios in which she ended up either injured, unconscious, or dead, so when her familiar purple mask came up on his display he nearly melted in relief. "Tali, I need you to reactivate the primary drive. We're turning EDI loose."

"Copy that, Shepard. On it." It was a testament to how much she trusted him that she didn't even hesitate. The seconds passed like hours as he waited, and then he heard the engines groan back to life. The low rumbling hum was like a symphony to his ears.

"I have control," EDI said, her voice taking on a smug tone that John had never heard before.

"Deletion of this program is not possible. You cannot—"

"You have messed with the wrong ship," EDI sneered, and blue waves of energy arced through the AI core as she took back the Normandy. The rogue AI screamed again, quieter this time, before dwindling into silence. "Commander, I have removed all traces of the hostile program and regained control of the ship."

"Thank you, EDI. Tali, you all right?"

"I'm fine, Shepard. Everyone down here present and accounted for. What about you?" she asked, her voice soft and worried.

"I'm okay. Get Jack and come up here to deck three when you can."

"Will do."

He went out into the mess hall and slumped against the wall. That was too close. Somehow, Tali had inadvertently picked up an unrecognized AI program powerful enough to control the Normandy from a century-old laptop. The very idea would have been laughable had it not actually happened. He still wasn't sure that unshackling EDI was a good idea, but maybe now he could get some answers. After all, she had his file in her systems somewhere; maybe she could help him find Doctor Bright and Able, and shed some light on this mess.