TITLE: Blinded by Science
AUTHOR: Wraithfodder
CATEGORY: Angst, drama
SPOILERS: Season two episode "Trinity"

Copyright Disclaimer: The Stargate Atlantis characters, as presented on the series, belong to MGM, Sci Fi, and other registered copyright holders. No copyright infringement is meant or intended by the writing and posting of this material. I'm just borrowing the characters and the universe for a piece of non-profit 'fan fiction' and will return in one piece (well, usually). However, all original characters and story material are copyright to author. Please do not repost this fiction, in whole or in part, anywhere, without expression written permission of the author.

SUMMARY: Takes place directly after the jumper return to Atlantis at the end of "Trinity." The damage is done. Can Sheppard's team pick up the pieces?

Blinded by Science

Author's note: This is just my interpretation on why Sheppard and McKay seem just 'not quite right' compared to season one… This was written after viewing "Trinity," but before seeing "Instinct," so hey, the following episodes could blow this all out of the water. Dialogue from part 4 of story is from the last scene of the episode.

Thanks to talbert6 for her beta-ing assistance!


Two minutes.

It was the longest two minutes in his entire life, getting back through the gate. Worse than when he'd flown the puddle jumper in a suicidal mission to destroy a Wraith hive ship. Worse than when the rotor on his chopper he'd been piloting in Afghanistan had been shot down by enemy forces and the craft had plummeted like a rock to the ground, crashing and throwing himself and his crew about like a child's toys.

Rodney's panicked side-seat driving in the fleeing jumper had escalated beyond mere distraction to the point that Sheppard had yelled at the man to just shut up. Worse, Sheppard had thought they could outrun the catastrophic overload that the Ancient weapon would create and double-back to the gate, but then Rodney screamed that three-quarters of the entire damn solar system was going to be obliterated in a matter of seconds. If the Daedalus hadn't shown up, they'd probably have been nailed by one of those weapon blasts trying to get through the gate.

The transition from the doomed planet's orbital junkyard to Atlantis' safe gateroom had been jarring. The gate was shut down immediately so there was no chance of any residual 'blowback' from the destruction of such a massive chunk of space. Just what was in that solar system? How many other planets, and god, were any of them inhabited?

The silence inside the jumper was deafening, because Rodney had lapsed into a state of perhaps guilty silence over what he'd done, or maybe because Sheppard was clenching his jaw so tight he was amazed he hadn't cracked any teeth yet. His mind felt trapped between terror of having just literally escaped dying and seething anger because he'd had to physically grab Rodney to shake common sense into the man.

Weir's uneasy voice crackled over the radio. "Are you two all right?"

"Yes," came Sheppard's terse reply.

"What happened?"

Sheppard didn't even deign to look at the subject of his roiling emotions. "Rodney blew up the damned planet, that's what happened."

It had been hours since the curt but tense debriefing with Weir, and what, really, was there for them to say? Sorry, made a mistake, hope nobody had any real estate in that part of the galaxy? Both men had been summoned to Weir's office immediately after debarking the jumper. Sheppard had just forced himself into a neutral mode, said as little as possible, and without any regret, left McKay there. In fact, it wasn't like he had much of a choice. Weir had had her say as to his participation in the fiasco – mostly in the form of a tongue-lashing in the disappointment category – and dismissed him. He knew that McKay was in for a helluva lot worse but didn't feel like sticking around to witness the fireworks. And he knew it would be worse because McKay still didn't seem to realize the implications of his actions.

Elizabeth had nixed the second mission in the beginning with very good reason. It was hard to rid his mind of the vision of Dr. Collins, his cooked body just steaming away on the floor of the command access tube. His skin was as red as a well-done lobster, and the smell…dreadful, but not as horrifically memorable as someone whose charred corpse was pulled from a burnt helicopter. And having to put in motion the proper channels so that Collins next of kin could be informed of his demise, but sorry, we can't say how or where he died and by the way, no, you can't have his body back… he pushed that bleak scenario from his thoughts.

But he knew that his words alone would probably not persuade Elizabeth to change her mind. When he spied Colonel Caldwell in a corridor talking with several of his people, he approached the man. It wasn't groveling, but presenting a different view on the experiment. He knew that Earth-bound interests were pushing for some bang for their buck. That was far from his own priority, which was the here and now and stopping the Wraith from devastating Pegasus and moving onto Earth.

Colonel Caldwell put his two cents worth into the case to continue experiments with the Ancient technology. He'd had a vested interest in a new weapon that could fight back or even eradicate the Wraith. Even Sheppard couldn't deny that any weapon to stop the Wraith from eating up the rest of the Galaxy was worth looking into. No matter, he still felt like he'd placed Elizabeth between a rock and a hard place when he'd said he protect Rodney by accompanying the scientist to the planet. But protect from whom? It was undeniable that Weir wanted Rodney protected from his own arrogance. Sheppard placed himself in that role and he'd grudgingly agreed to the mission. She knew, as Sheppard realized, that eventually the SGC would order experiments to continue once word got back to Earth on the incredible power source.

He'd trusted McKay to do his best, but not to plow ahead heedless of escalating power surges that were going to get them killed. Rodney had asked for his trust – had pleaded for it – and even with the incredible risks, Sheppard had reluctantly given it. Yet after Zelenka had expressed serious reservations on continuing the experiment after presenting his calculations, Rodney had angrily dismissed him, but guaranteed Sheppard that he knew what he was doing. But he hadn't.


The scuttlebutt about Weir's earsplitting dressing-down of Rodney McKay in her office had spread throughout Atlantis like the shockwave of a nuclear bomb. The analogy was perversely appropriate: after all, the disaster had been even beyond the magnitude of destruction that kind of weapon could create.

Yet Sheppard had found it easy not to deal with it. When Rodney's voice filtered over his earpiece, Sheppard chose to ignore it. He wasn't in the mood to say something he might later regret and he knew that in the state of mind he was currently in, there was a very strong chance that words of that sort would be said.

Instead, he'd explained the disaster to Caldwell, promising the man a finished report later. It was not something that he was looking forward to writing. He knew that Caldwell's superiors on Earth would be even less pleased to know that a potential weapon against the Wraith was now gone forever, but in reality, would it have ever worked?

Sheppard paused in the corridor he'd been aimlessly walking along, then rubbed fingers deeply at the bridge of his nose. A headache was working its way in, promising him a sleepless night.

After a moment, he realized that he wasn't far from the workout room where he frequently sparred with Teyla. Although he hadn't brought his equipment, it was also a place he could simply just sit and be alone, or maybe kick the walls with wild abandon. He wasn't sure which he wanted to do more in order to sort out his conflicted feelings.

He entered the room, surprised to find Teyla already there. He hadn't realized she'd returned from the trading mission to Belkan. Damn, he felt out of the loop. Teyla was in her workout gear, facing the opposite wall, oblivious to his presence. She aggressively moved into a pose, sticks at the ready. Abruptly, she pulled back into a standing position, screamed in frustration, then turned and threw the sticks.

"Dammit!" swore Sheppard angrily. He rubbed at a spot where a stick had struck his shoulder. "What the hell is your problem?"

Teyla was startled. "Colonel, I—" She moved forward, then halted as though unsure how to proceed. "Did I hurt you?"

"Just my pride," he grumbled. He picked up the sticks that had landed next to him, handing them back to her. "Should have dodged those flying objects. Good thing it wasn't a Wraith stunner blast."

"I am sorry," she apologized.

"Well, at least I'm here to get hit by sticks." Sheppard suddenly didn't feel like sorting out his emotions by kicking walls. He sat down on the padded bench by the window, drawing up one leg as he leaned against the wall.

"I understand that not all went well on your mission to Duranda." Teyla gathered a towel from her kit, wiping the sweat from her face.

"Well, that's the biggest understatement of the galaxy." Sheppard rubbed a palm against his forehead, wishing he'd never answered Rodney's knock on his door earlier that day. "And how was your trip?"

He heard a 'hmmph' noise back in response. He opened his eyes slowly, watching curiously as Teyla dumped her exercise kit in between them on the bench and sat down. "What? Flax bean shortage? Price gouging?"

"Let me just say that negotiations the next time will not be as amenable." Teyla forcibly jammed a stick into the bag, making Sheppard wonder whom she really wanted to do that to.

"What happened?" he asked. God, he'd actually welcome news of a simple ordinary ran-into-a-Wraith took-care-of-it tale.

"Ronon participated in the negotiations."

Sheppard frowned, puzzled. He'd known that Teyla had taken the Satedan weapons specialist with her on the mission, but Ronon was not a negotiator, at least not when it came to mincing words. His idea of negotiation – if their experience on Olesia was any indication - was done with weapons, usually a gun, pointed at someone's head. "What did he do?"

Teyla didn't meet his eyes for a moment, staring into the depths of her bag as though maybe the answer lay there. He wasn't sure if he wanted to know what was bothering her so much. "He drew a knife. He did not make an overt threat, but the intent was there," she replied. "I managed to smooth things over, but the next set of negotiations will be… uncomfortable."

Well, crap, that wasn't good, but at least Dex hadn't blown up a whole damned world. "Anything else I should know?" The man hadn't been on Atlantis very long. He was a good soldier, but in some respects, he was still an unknown quality, and right now, Sheppard's trust in those close to him had taken a nasty hit.

Teyla hesitated a moment. He detected a dark flicker across her eyes, but again he wasn't sure what she was thinking about, probably because he was still thinking too much about Rodney's nearly obsessive cry of 'Just one second!' after Sheppard had ordered him to stop. "Ronon is not the only survivor from his world," she replied at last. "Apparently over 300 of his people managed to survive the Wraith attack, and have scattered across various worlds."

Sheppard arched an eyebrow, the implications of that statement running a flurry of scenarios through his mind. "Will he be joining them?" A logical question, considering how morose Dex had appeared upon viewing his desolated home world.

"I do not think so."

Sheppard waited for more, but Teyla remained incredibly silent. Okay, so something hadn't gone down well on that mission. It could be the knife incident, or the ruination of a good trade relationship, but he sensed it was something more than that, yet didn't feel like pressing, at least not yet.

Teyla looked up from the bag. "Did the explosion truly destroy part of a solar system?"

Sheppard stood abruptly, pacing over to the other side of the room. He ran both hands hard through his hair as he tried to get his thoughts in order. "Not just one planet, but a couple others as well," he replied tersely.

Teyla drew in a startled breath. "They were not inhabited…"

"No." He'd found Zelenka after the debriefing. Had him double-check the Ancient database. Fortunately the two planets within the projected radius of destruction were uninhabitable and even 10,000 years of planetary evolution wouldn't have changed that fact. It was one thing to kill over 50 men by putting up the gate's shield to defend Atlantis, but Sheppard didn't know how he could deal with genocide on a planetary scale, even if it was unintentional.

"That is good." Teyla sounded relieved.

But then what had Rodney talked about on the way to Elizabeth's office? How the experiment should have worked – he was still convinced, on some unfathomable realm – that Project Arcturus was not a failure, and that if nothing else, at least they were okay.

And it had been that last, almost casually tossed-off statement – as if making light of their near death would somehow lessen the horror – that had locked Sheppard into a stonewall of silence. If McKay had been one of his men, a soldier, he would have reamed him out worse than Weir had done. Hell, he might have even decked him down on that planet. He had an explosive temper, he knew, but it took a LOT to drag it out of him.

But McKay wasn't a soldier.

Sheppard paced to the next wall. He spied a ball that someone had left there and aggressively kicked it. The ball ricocheted off a couple walls, narrowly missing Teyla in its path. He realized his mistake too late, but in response, the Athosian simply arched an eyebrow in a reproachful manner, indicating her ire at his recklessness, but also her understanding.

He directed a short but apologetic smile her way, then paced again. He felt trapped within himself.

"I'd be dead. McKay would be dead. If I hadn't dragged him out of there," he continued. "Just one more minute, just one more second." He almost spat out those phrases, remembering how McKay kept frantically uttering them as the installation was literally falling down around their heads. Sheppard focused his angry gaze at the ball once more. "The damned idiot was just obsessed with making that weapon work no matter what the cost."

"He has always been preoccupied with his work," observed Teyla.

"But not obsessed," countered Sheppard hotly. "Not to the point…"Where if McKay hadn't finally obeyed, Sheppard might have hit the man to knock some much-needed sense into him. He couldn't help but remember some of General O'Neill's remarks in Rodney's file folder – he'd seen it after taking him onto the team – in which O'Neill made some less than flattering remarks about the scientist's obsession with getting a broken Stargate working – even at the risk of 'erasing' the SG-1 team member, Teal'c, who was trapped in the gate's 'buffer.' Rodney had changed in the time he'd known him on Atlantis, but was he back to that attitude now? Science over life? Or had he always been like that and Sheppard just hadn't seen it?

The ball rolled in a tantalizing pattern near his feet. He focused his frustration on the thing, kicking it again, but at a trajectory he knew wouldn't go near Teyla.

"We could be dead. Hell, all of Atlantis could have been obliterated if that planet had blown with the gate open."

Sheppard watched the ball come to a stop in the far corner, as if leery of getting near him again. Teyla stood, gathering her bag. "I am going for a walk."

Sheppard stared in puzzlement. "Where?"

"Some place quiet."

Sheppard let the hint of a tired smile touch his lips, hoping that the unspoken invitation he'd detected was there. "I know just the place." He strode over and grabbed the red ball. "C'mon, Wilson."

End of parts 1 and 2.