A/N: This is the start of a long, LONG, epic Academy fic.

I love plot holes, and here's a biggie:

Pike: "And if all else fails, fall back and rendezvous with the fleet in the Laurentian system. Kirk, I'm promoting you to first officer."

Huh? I mean, that doesn't make any sense! Jim's just an untried cadet, and surely there are more seasoned officers on the Enterprisewho should be first officer. Unless… does Pike know something about Kirk that we don't? If he does, it must be pretty compelling…

That got me thinking, and it was the inspiration for this fic.

This is the story of a friendship between two men who are thrown together by chance (and no, I don't think that the shuttle ride was the start of a beautiful relationship) and are forced to depend on each other when circumstances spiral completely out of their control. There's going to be plenty of whump (yay!), angst, Tarsus, and adventure. Plus a bunch of TOS references and rebooted characters.

I'd like to thank three people who are helping me tremendously on this project:

Caera1996, my number one beta, brainstormer, and cheering section;
Ggo85, who points out all the inconsistencies and problems in my writing, and reminds me frequently that Starfleet is a military organization filled with competent officers;
And StillWaters1, a registered nurse and talented writer who agrees with me that even in the 23rd century, the human body can't be healed with a magic hypo and a dermal regenerator.

So… enjoy!

Title: We Two Alone

Come, let's away to prison;

We two alone will sing

- William Shakespeare

Part One

Starfleet Academy, Summer 2257

Jim

Even before he opened his eyes, Jim could tell that something was really wrong.

His limbs felt heavy with exhaustion, as if he wasn't waking from a full night's sleep, and a headache was gathering at the base of his skull. As he turned his head on the pillow, he felt a sharp stab of pain at the juncture of his neck and shoulder. Ouch.

Taking a slow, deep breath, he sat up carefully, massaging his neck. He squinted against the morning light filtering in from the window. It seemed slightly out of focus. He blinked and rubbed at his eyes, but the world stayed blurry. He felt feverish.

And wasn't that perfect, because if there was one thing he didn't have time for today—or this week, for that matter—it was the flu.

"You look like hell," Dan Corrigan, his roommate, confirmed as Jim groaned his way to the bathroom. Corrigan was already on his feet and getting dressed. "Thought you got in early last night."

"I did." In fact, he'd turned in before ten, feeling inexplicably tired after his hand-to-hand session. Cupping his hands, he splashed cold water on his face, then bent his mouth down to the faucet. The cool liquid soothed his throat. "Hope I'm not coming down with something."

"Better perk up then, Kirk. Don't you have class this morning?"

"Diplomacy seminar," Jim muttered. Six hours of small-group discussions, student presentations, and simulations. Ordinarily, he'd be up like a shot preparing for his day, reviewing the assigned readings and going over his notes for his presentation. But this morning he felt so sluggish and depleted that he could already tell that he'd have to detour by the cafeteria for a strong cup of coffee before the seminar. At the rate that he was going, that meant that he'd barely make it to class on time. Not good.

"Summer session, and you're still in class all day?" Corrigan said, sounding smug. "Should've gone for the biosciences. I'm in the lab for a few hours this morning, but then I'm free."

"Shut the fuck up, Corrigan," he grumbled, lacking the energy to think of a clever retort. He peered at his pale, splotchy reflection in the mirror. Can't skip the shower, he decided. It might save him a few minutes, but if he walked into his seminar looking this rumpled, Commander Billings was likely to use him as the focal point for an off-the-cuff lecture on proper grooming and the importance of maintaining a respectful appearance. And he really, really did not want to attract attention today.

The hot shower woke him up a little, but did nothing for the ache in his neck. He shrugged into a fresh uniform, then sat down to fasten his boots. His head pounded as he bent down, a pain that focused at the base of his skull and radiated down his neck. Massaging the taut muscles, he straightened back up awkwardly, doing his best not to move his head.

Should've done more stretching after the workout yesterday, instead of rushing back to the dorm, he thought in disgust. A stiff neck would slow him down all day, throw off his concentration.

Can't afford to make stupid mistakes this week, dumbass.

The boots finally on, he sat back and took a deep breath. Even the minor effort of getting dressed had left him a little breathless. His temples throbbed. Sighing, he glanced over at Corrigan, who was sitting on his bed, scanning the morning news feeds as usual. "Got anything for a headache? Or a fever?"

Corrigan gave him a curious look. "That's got to be a first for you. Jim Kirk, admitting that he needs meds? You wouldn't see a doctor even when you had bronchitis last winter."

"It was a cold," Jim huffed. "And I'm from Iowa, man. We don't get sick."

"Sure you don't," Corrigan laughed, but his expression was sympathetic. They weren't good friends, but they helped each other out when they could. "I don't have anything here in the room. But you should hit the clinic before class. One hypo, and you're good as new."

Jim shook his head. He knew a fair number of cadets who would head off to the Academy clinic at the first sign of a sore throat, hoping for a quick fix or, at the very least, a medical excuse to lie in bed for a day or two. Corrigan, for example, was a borderline hypochondriac from L.A. who popped a pill every time he got a sniffle, which was just pathetic, as far as Jim was concerned. Jim avoided doctors whenever possible and hadn't seen the inside of the clinic since his last physical, a year ago.

There was no big mystery behind it. He grew up knowing that being sick wasn't something that would get him a cozy day in bed. Even now, he could hear his uncle's derisive shouts echoing through the farm house: I don't care what the hell's wrong with you, get your lazy ass outside and start your chores, and don't give me that lip. But Frank's attitude wasn't really that different from what he heard from his grandparents and most of the adults in Riverside, a mixture of stoicism and Midwestern work ethic, and by now, it was a point of pride.

So he just rolled his eyes. "Never mind, I'm not that desperate. And I can't risk getting grounded."

Corrigan shrugged. "Tough it out, then. I'm off to the lab." He slapped Jim on the back on his way out the door. It was probably meant to be encouraging, but it made Jim grit his teeth at the jolt of pain that radiated out from his neck.

After another minute, Jim stood shakily, tucked his PADD into his jacket pocket, and headed to the cafeteria.

The coffee picked him up a little, but by noon, Jim couldn't deny that he was sick: he was alternately burning up or chilled. The muscles of his calves and thighs were starting to ache, as if he'd been exercising hard, and not just sitting in a classroom. He desperately wanted to go back to bed.

The soreness in his neck made it hard for him to look down at the PADD in front of him, and even when he managed it, the letters on the screen seemed to be out of focus. And for that matter, the instructor looked a little blurry around the edges, too. He kept blinking, trying to clear his vision.

"Am I boring you, Mr. Kirk?"

Jim snapped back to awareness with an unpleasant jerk that sent a sharp pain through the back of his skull. Damn it, he must have nodded off. He glanced around, registering that all eyes in the classroom were on him, and he straightened himself in the chair, suppressing a wince. He could hear muffled laughter from somewhere behind him.

"Uh, no, sir. Sorry." The truth of the matter was that Commander Billings was a tedious lecturer, droning on and on with a monotonous nasal voice, but even in his feverish state, Jim wasn't dumb enough to say so.

"Would you like a pillow?"

Asshole. "That's not necessary, sir." He wiped a shaky hand across his forehead; it was damp with sweat.

Billings swept his gaze around the classroom. "Diplomacy can put you to sleep, no question about it. Negotiations often drag on for hours." He fixed Jim with a pointed look. "Even so, your job at Axanar is to remain attentive and focused, no matter how dull you may think the speakers are."

"Yes, sir," Jim said, and was relieved to see his classmates turn their attention back to Billings, as he went on with the discussion.

The Axanar Peace Mission was the culmination of a full year of galactic diplomacy. For the last month, since the start of the summer session, the cadets had been immersed in the political and economic background of the area, including the Battle of Axanar and its aftermath. Jim, along with the other command-track cadets, would be working behind the scenes as assistant diplomatic attachés. He'd been more excited about the role until he found out what it really meant: taking notes, running errands, and observing the official delegates.

But in the end, he decided he didn't care what he'd be doing at Axanar. The highlight of the trip, as far as he was concerned, was the opportunity to train on a starship. They'd be travelling on the Farragut, Starfleet's newest Constitution-class ship. Three weeks there and three weeks back. Last summer's training, after his first year at the Academy, had been basically an introduction to ship life and routines, and the ship had never left the solar system or even attained warp speed. This would be his first long-term shipboard training, and his instructors would be watching everything, all the time.

Jim was determined to stand out. The cadets would be rotated through most of the main operating systems: helm, engineering, communications, weaponry, even administration. Their performance on the trip would play a large role in determining the direction of their specialized training over the next two years at the Academy. Jim was ready for all of it, dying to prove himself.

Commander Billings was expounding on Captain Garth's military strategies in the battle against the Klingons, normally something that would have riveted Jim's attention, but his thoughts kept drifting. He knew that he was ill, and it was coming on fast and strong. The ache in his neck was getting progressively worse.

It might be a 24-hour virus, he told himself. Anything else just wasn't an option. The Farragut was leaving in three days, and he had to be at the top of his game.

When the seminar finally broke in early afternoon, the other cadets rose quickly, heading for lunch, laughing and chattering. Jim was usually one of the first out of his seat, impatient with restless energy after sitting still for so long, but today every movement jarred his neck and he didn't have the energy to move fast.

"Mr. Kirk," he heard Billings say as he finally turned to leave, and he suppressed a groan. The last thing he wanted right now was a reprimand from his instructor. Damn it, he knew he hadn't been paying attention, but he thought he'd been faking it pretty well, except for that time he nodded off…

"Yes, sir?"

Billings gave him a sharp look, then said quietly, "You don't look well, and you certainly weren't yourself in that seminar. Are you feeling all right?"

Jim looked back at him, surprised at the show of sympathy. It was the first time he'd seen a side of his instructor that was anything but stern and by-the-book. It was actually a little disconcerting, making Jim loosen the tight hold he'd had on his emotional control all morning. "I'm a little under the weather, sir, that's all." His voice wavered a bit-Damn it, must be the fever—and he took a breath. "Thank you for asking. I'll be all right."

"Go to the clinic during the break, Kirk," Billings said firmly. "Get yourself seen by a doctor. You've got ninety minutes before we start the student presentations."

"That's not necessary, sir. I'll go after class." The only thing he wanted to do right now was go back to his dorm and take a nap. He'd muster the energy to go to the clinic later… if he really had to.

But Billings just waved a hand impatiently. "That was an order, Mr. Kirk."

Damn. "Yes, sir." Jim saluted half-heartedly and left the classroom.

Well, Billings was probably right, anyway. Whatever was wrong with him, it didn't seem to be going away, and he needed to do something about it. He could tell that his fever was climbing higher, because it was becoming an effort just to sit in his seat and keep his eyes open. His head had been pounding fiercely for the past two hours. He probably just needed an antiviral hypo, and maybe a muscle relaxant for his neck. He hated doctors, but they could be useful. Why drag this out? He'd come back for the afternoon session, good as new.

But at the Academy clinic, no one seemed to care that he was in a hurry to get back to class. Jim sat shirtless and uncomfortable on the biobed while the doctor on call asked him the standard intake questions. Dr. Grace Levine was a middle-aged, methodical, can't-be-rushed type, and Jim found himself checking the time more than once as she asked him about his symptoms and reviewed his medical history.

"Lie down," she told him. "Let me see what the scan shows."

He couldn't see the screen above his head, so he watched her face instead. At first her expression was bland as she gazed at the screen, but after a moment the doctor's eyes narrowed and she pursed her lips, frowning at something she was seeing.

"What is it?" he asked nervously. "What's wrong?"

"One moment, Cadet," she said. "Lie still. You have a fever of nearly 39 degrees. And there are some signs of inflammation here…"

"Where?" he asked. Instead of answering, she leaned forward to adjust something on the monitor. Jim took a deep breath and made an effort to relax. He knew the doctor was scanning his vitals, and his blood pressure was probably climbing through the ceiling. Fuck, he hated being out of the loop. Doctors were like that, never coming clean with everything they knew, only revealing bits of information that they thought you needed to know.

Scan complete, Dr. Levine began a physical exam, which Jim endured with barely concealed impatience. He felt tired and irritable, and not at all convinced that he'd made the right decision in coming to the clinic. He closed his eyes against the glare of the lights as the doctor felt his glands, palpated his abdomen, and examined the skin along his torso.

"Bend your head forward," she said finally. "Try to touch your chin to your chest."

It was surprisingly difficult to do, even with Dr. Levine gently supporting the back of his head. His knees flexed involuntarily in an ineffective attempt to relieve the piercing pain that lanced down his back. "Fuck!" he gasped. "Sorry, damn it, my neck's really stiff. I should have done more stretching after my workout yesterday…"

"I don't think that's the problem," she said with a gentle sympathy that set his teeth on edge. "I doubt very much that it's muscular strain."

"What do you-"

"Just a minute, Cadet Kirk." Jim rubbed his temples in frustration as she scribbled on a PADD. God, he felt like shit. His headache was getting worse, and now his stomach was starting to feel queasy. He glanced at the small basin on a tray by the side of the bed, thinking that he might have to grab it in a hurry if he needed to throw up. He concentrated on taking shallow, even breaths, wishing fervently that the doctor would just hurry the hell up so he could get out of the clinic.

Dr. Levine finally tapped the PADD with a nod of satisfaction. She plucked a vial from a shelf and fitted it into a hypospray with a click. "I'll give you something now for the fever and the headache while we wait for your transport."

"My transport?" he repeated dumbly, feeling like he'd missed something. "Transport where?"

"Starfleet Medical." She pressed the hypo against his neck, but he was so distracted by what she was saying that for once in his life, he didn't even feel the sting. "You need a more thorough workup than we're equipped for here at the clinic."

"Wait, what? Are you serious?" he sputtered. He raised himself painfully into a sitting position. "No way! That's not necessary, and I'm…" I'm fine, he almost said, but that was obviously not true. "I'm late. I don't have time to go anywhere right now." His seminar was starting again in ten minutes. "I'll come back later this afternoon if it's not better, I promise. But right now I've got to get back to class."

Levine's eyes were understanding but her tone was firm. "I'm sorry, Cadet Kirk. I know this probably doesn't fit into your plans, but you really don't have a choice here. Once you walked through the clinic doors, I'm responsible for your treatment, and my decision is that you need to be transferred to Starfleet Medical."

"But I can't go to the hospital!" Jim told her, a little desperately. This was exactly the reason he tried to avoid doctors in the first place. The second he stepped onto their turf, they took over and started making decisions for him, without any consideration for what he wanted to do.

Getting hysterical isn't going to help, idiot.

Making an effort to rein in his frustration, he lowered his voice and spoke as calmly as he could. "With all due respect, I think you're overreacting. I just came in here to get something that'll pick me up enough so I can concentrate in class. I don't need to be coddled." He gave the doctor his most persuasive smile, for good measure. "So thanks, but I'm feeling a lot better already…"

"I'd be surprised if you weren't. I just gave you a strong painkiller," she said. "This is potentially quite serious and no, it can't wait."

Her words chilled him—I can't get sick now!—and he took a deep breath, trying to mask his worry. "So what's wrong with me, then?" he asked, a note a fear creeping into his voice. "It's not classified information, is it? Just tell me."

"I suspect some form of meningitis, but I can't start treatment until we make an accurate diagnosis."

"Meningitis?" For a moment, he just looked at her in astonishment. He'd been so sure it was the flu. Shit, no wonder he felt so bad… He'd heard of babies and small children who got meningitis, but nobody his own age. Wasn't it one of those ancient diseases that was eradicated ages ago? "But… it's treatable, right?"

"Usually it's just a matter of a simple course of antibiotics or antivirals." She gave him a quick smile, obviously intended to reassure him. "I'll inform SFM that you'll be arriving on a priority transport."

"Yes, ma'am," he said glumly. So fifteen minutes later, he was sitting on another biobed in a small exam room at Starfleet Medical, shivering in a flimsy medical gown and wondering how he was going to convince the next doctor that he really, really needed to be cleared to go to Axanar.