Summary: Harrison is back and he's not planning on retiring to Risa. The crew of the Enterprise may be humanity's last hope as the return of the augments incites the Second Eugenics War.

Beta reader: LJ user Siluria.

Disclaimer: I don't own Star Trek or any of its characters, Paramount does, and didn't create them either, Roddenberry did.

Author's note: This is still a WIP, so the warnings might change for later chapters. Spoilers for Star Trek into Darkness.

– The Second Eugenics War – Chapter 1 –

"Ambassador, I can assure you, Khan and all the other augments from the Botany Bay are constantly monitored. This is a secure facility!" Admiral Darbo said as he strode through the wide hanger doors to the holding bay containing the cryogenic pods. Ambassador Spock was at his heels.

"Well, you must forgive an old Vulcan his foibles."

Darbo gave Spock a questioning look, but said no more until they had reached the exact pod they had come to inspect.

"Here it is," the Admiral said before wiping the condensation off the outside of the cryo chamber to reveal the occupant's pale, angular face.

"This," Spock stated before looking up and fixing his eyes on Darbo's, "is not Khan Noonien Singh.

###

Two weeks later.

"When you and your crew beat me, I briefly considered whether maybe I was not as superior as I had thought. Maybe the human race had evolved in some way since I'd been frozen." John Harrison's words sent a shiver down Jim's spine, although he'd listened to this recording over a dozen times already.

"You are all just as weak as I remember though. The evidence of this is staring you in the face right now: I'm awake again. You should have killed me when you had the chance. No, really, you should have. Now someone else hopes to use me as their pawn. I think you have some idea how that might work out for them. Goodbye, James T. Kirk."

On the small screen in Jim's quarters, Harrison's face was replaced by the Starfleet logo. And Jim groaned. He'd received the communication less than an hour ago and had already watched it multiple times. Last week Admiral Darbo had reported that the augments had all vanished from their pods. Ever since Kirk had been dreading that Harrison would get in contact. At least he hadn't gotten in contact via beaming a photon torpedo into the engine room.

"Tell me, Spock," he asked the only other person in the room, "what should I make of this? Who is John Harrison even?"

Spock took a step closer so that he was standing next to Jim, at his desk. "An augment. One of the 73 people that were found onboard the Botany Bay."

"Yes, but those augments, they included tyrants and war criminals. Khan is among them, but Harrison is not him. Your counterpart confirmed that."

"Someone has freed all the augments—beamed them right out of their pods using the trans-warp beaming equation, to be exact. Yet I have noticed that you have been especially preoccupied by Harrison's true identity. Why?" Spock asked.

Jim turned away from the screen, walked over to a bookshelf, and grabbed an old-style paper book.

"In here," he said, waving the book in front of his first officer's face, "is some of the history of the Eugenics wars. It chronicles the rise of Khan Noonien Singh, who's empire stretched all the way from Shanghai to Melbourne to Beirut—and the rise of his greatest rival, Harrison Vear, ruler of the Second British Empire. Khan was a tyrant who gave his citizens no freedom at all. But he gained control of over 40 Earth nations and managed them without a single massacre. There was no civil unrest. A fascinating man! Vear on the other hand slaughtered people in the millions. He treated those who weren't augments as if they weren't actually people."

"You suspect, then, that John Harrison is Vear?"

"I don't know. I'm not sure. Why would he pretend to be Khan?" Jim put the book back. "I guess it hardly matters, as we already know what Harrison is capable of, and what his views on non-augments are. But-"

Spock raised an eyebrow to prompt Jim to continue.

"But if I have to face him again, I want to know as much about Harrison as possible." Jim stood in front of Spock and narrowed his eyes slightly. "And I will not let him use me as some kind of puppet."

"I'm sorry I cannot offer a solution to that particular problem," Spock replied, eliciting a snort from Jim, "I suggest though that we analyze this recording in detail to pinpoint from where it was sent, and when."

Jim nodded his head. "Agreed. Sort that out, Spock. In the meantime I'll be on the bridge. We should be coming into orbit around our first unexplored planet soon. Maybe we will be able to do some actual exploring for once."

###

The planet's surface was windy, but the air still had a stale taste to it. They'd measured large contents of ferric oxide particles in the atmosphere before landing, so the sky's color was no surprise, but nonetheless the bright scarlet dome overhead took Jim's breath away.

Nothing like a new world to take my thoughts off Harrison, Jim thought.

A small team up on the ship was analyzing the message he'd been sent. Nothing he could do until they'd finished. He took his eyes off the sky and checked his away team were okay. He'd taken two security personnel, Spock, and Carol down with him. She was still science division after all.

"Dr. Marcus, is anything wrong?"

Carol was staring down at her tricorder, her brow furrowed. Jim glanced at the others as he hurried over to her, removing his own tricorder from his belt mid stride—Carol wasn't the only one worried.

"Down!" Spock shouted.

Weapons light zipped overhead accompanied by a buzzing sound as they all threw themselves into the sand. Jim and Carol were about an arm's length away from one another.

"It's coming from over there," Carol said, indicating to the right with her head.

"Everyone get behind those boulders!" Jim shouted. He hoisted his phaser out of its holder and started firing in retaliation.

As they scrambled to safety Jim saw a woman from security go down. Spock had his communicator out and was hailing the Enterprise.

Jim grabbed it off him. "Scotty, get us out of here!"

A flash of blinding red light lit up Jim's vision.

###

"He can't be waking up already, man, he took a disruptor shot to the chest!"

That was Bones, Jim was certain of it.

"Take a look for yourself," another voice cut in.

Footsteps.

Then, "Jim? Talk to me, kid."

When Jim opened his eyes a bit he could see Bones clearly. "Disruptor fire? Was it Klingons?"

"Shut up. I'm still healing your wounds. You should be dead from such a wound, you know that, right?"

"That's what you always say, Bones."

He closed his eyes again and let his friend treat him. The humming and beeping of the tricorders kept his mind in the present though. Should be dead. Was this one of Bones's usual exaggerations, or did he actually mean it? What had they done to him when they'd given him an infusion of Harrison's blood? It wasn't cold in sickbay, but he could feel his skin prickling as his hairs stood on end.

Finally the whirr of the medical instruments subsided. Jim tried to sit up, but Bones reached out to put a hand on his shoulder to gently coax him back down. "Not yet," the doctor said sternly.

"What happened? Where are the others?" Jim asked.

"I am right here, Captain."

Jim turned his head. Not six feet away from his bed Spock stood with his hands clasped behind his back.

"He still needs rest," Bones started to protest.

"Commander Spock, report," Jim said curtly.

He couldn't see, but he knew Bones was rolling his eyes. If the situation weren't so dire, that knowledge would have made him grin.

"A group of Klingons, Captain. We estimate about twenty on the planet. Presumably they have a ship in this sector, or even in orbit, but our scanners have not been able to pick up a signal so far."

"Any casualties?"

"Lieutenant Xu did not survive, sir."

But I did.

He clenched his jaw. "Check on the progress of the recording's analysis and find the Klingon ship." A hypospray was jabbed into his neck. "Ouch! Bones, was that really necessary?"

"No, I poke you with these things for fun. Of course it was necessary!"

"Help me up."

At that request Bones paused in what he was doing and Spock stepped closer.

Then a litany of "You should rest," and "Are you out of your goddamned mind?" along with other such curses and logical arguments followed his request.

Jim held up one of his hands. "Enough!" He fixed both his First Officer and his Chief Medical Officer in turn with a hard stare. "Someone out there is armed with both the trans-warp beaming equation and augments. We were just attacked by Klingons that seemingly got onto a planet without a ship that is really fucking far away from their homeworld—the one place off Earth that we know for sure Harrison visited. Now, are either of you going to let me report this directly to Admiral Darbo, or waste time fussing over this scratch on my chest?"

After saying all that he found himself panting. Oh-oh. I shouldn't have said that last bit. On cue his friends both continued their protestations. Eventually though they did fetch him a wheelchair.

###

Jim looked around the table in the conference room at his senior staff, only Scotty was missing.

He hit a key on a comm panel in front of him. "Mr Scott. Where ar-."

"I'm coming, I'm coming! Would ye rather I made sure the warp engines continue not to blow us out of time and space, splattering our atom fragments across the skies of half a dozen or so planets, or that I was on time for one wee video call?"

"Sir," Uhura said, "the admiral's call is coming in now."

"Put it on screen. Scotty, hurry up."

Admiral Darbo's face was glistening with sweat. "Captain Kirk, we received your message and have discussed its content in an emergency meeting. Have you since completed the analysis of the message Harrison sent you? Have you taken any of the Klingons on the planet into custody?"

Jim cleared his throat before speaking. His mouth felt dry. "The message came from Qo'noS. There is no doubt that Harrison was, at that time, on the Klingon homeworld. And we've captured none of the party that attacked us. We're no longer registering any Klingon lifesigns from the surface."

"You measured none before you beamed down, is that correct?"

"Yes sir. Our initial scan of the planet found it to be uninhabited."

"We will investigate whether there was a security breach here at Starfleet HQ as you requested."

"Thank you, Admiral. Very much appreciated."

Darbo sighed. "I was hoping you wouldn't tell me Harrison's message came from Qo'noS. Anywhere but from there."

Jim became aware that his fingers were hurting. He'd clenched them into fists under the conference table.

"Send us a full report of that analysis. Immediately. If we verify your people's conclusions then I am not sure whether or not this might be taken as a full scale declaration of war with the Klingons."

"But sir!" Jim jumped up out of his wheelchair and immediately winced. Spock was at his side in under a second, stabilizing him. "These are Harrison's actions. We don't know if the Klingon High Command have any knowledge of his existence!"

"We have already dispatched a message informing them that Harrison is a convicted war criminal and requesting that they extradite him and all the other augments back to us. We should receive a reply shortly. I will keep you informed. In the meantime you must keep your shields up at all time, even when at warp."

"Understood," Jim wheezed as he sat down again slowly, Spock holding his shoulders tightly all the while.

"Good luck. Darbo out."

To be continued...

A/N: Thanks to Nathalie for pointing out that screwed up my formatting.