Jim Kirk sat in a room full of Starfleet admirals as he listened to Admiral Winston begin to explain what had happened. "I might as well start at the beginning," Admiral Winston said. "I'm about to give all of you a history lesson about Starfleet that you don't know. It's always been said that Starfleet started from the space program, but in fact, it was once called the G.D.I. which is Global Defense Initiative. It started out as a military operation."

Jim had a serious case of déjà vu, as he remembered Scotty saying this is a military operation. "Why was this not brought out before now?" he asked.

"Because we had not heard from Kane or any of his followers. It was thought that keeping it secret would be best except for the head of Starfleet. Admiral Kirk, you were closer to being part of that than any of us."

"How so?"

"When Admiral Marcus sent you out there to Klingon space to kill Khan, he didn't want you to bring him back to Earth, because he would have told everything. Khan knew because he was part of the Nod. When they were defeated, and Khan was gone from the Earth, the war ended. Admiral Marcus searched for the Botany Bay which was the ship that Khan escaped in, because he wanted to find Kane and get the Scrin knowledge from Khan. He searched for it for years because he thought Kane was with them. You see, Kane was one of them…the augments. We figured Kane was with them, frozen in time somewhere too. That was how he had survived all those years."

"This sounds crazy," Jim said. "Are you telling me that Admiral Marcus stranded me and my crew in Klingon space and tried to kill us because he was afraid Khan would tell everything he knew about this war?"

"That's it."

"Did you know about it?"

"Of course not. You remember, that mission was only between you and Admiral Marcus. You were going on his own personal agenda as well as your own."

Jim could not deny that. "You're right there."

"See, Khan had Scrin knowledge for weapons, and that was why he destroyed that facility. It was to stop Marcus from getting his hands on that technology. He was also doing research on Tiberium which can be used to create incredibly powerful bombs if it's isolated properly. He wanted Khan to help him so he would have superior weapons to the Klingons and also to be ready for the war he thought was coming with the Nod."

"Well, obviously, he was right," Jim said. "That thing took over the Enterprise with no effort at all."

"Cabal."

"Yeah, just what is that thing?"

"I'll get to that. You know, Marcus was afraid you would find out everything, and after everything happened, I figured he thought you would steal all his glory if a war broke out."

Jim could remember Marcus saying, "I was never gonna spare your crew." Jim looked at Admiral Winston. "He thought I would figure out everything? How did he think I could do that?"

"Well, Admiral Kirk, you have to admit, you have figured out much more than most people. Khan destroyed that facility not only because he wanted to stop the research but because it contained the history of the GDI and the Nod. It wasn't just a library and it wasn't just a research facility…it was both."

"I've never heard of any of this," Admiral Shawn Greene said. "It's rather disturbing that this was kept secret from all of us."

Admiral Winston sat down. "It's out now," he said. "Going on about why it was kept secret won't get us anywhere."

"Hiding history doesn't make it go away. It causes it to be repeated. Look where we are now: an unexpected attack, and they have control of Headquarters."

"We can't blame all that on Admiral Winston," Jim said.

"Why not?" Admiral Greene asked. "You probably knew about it yourself."

"I did not. They took over the Enterprise to get here, and we couldn't stop them. You think I wouldn't have prevented that if I could? Besides, this arguing isn't getting us anywhere." Jim leaned on the table and looked at Admiral Winston. "How do we stop this? What are they after?"

"I'm getting to that," Winston replied. "GDI Headquarters was in the same location as Starfleet Headquarters. That's why they wanted to take it over. However, they won't find what they're looking for. All the information they want is stored here in a completely different database. They're also most likely trying to find the ion cannon, but it's not there either."

"Ion cannon? What is that? And where is it? Should we be worried about it getting into their hands?"

"No. It is not accessible from where they are. It's actually housed in the Earth defense mechanism. It was the most logical place to hide it, but it hasn't been activated in years. It takes time to bring it online. The last time it was used was when Khan and his crew were escaping in the Botany Bay. Starfleet tried to destroy it with the ion cannon, but of course, they got away. When that ship was found, Kane wasn't on it, so we're assuming that Legion and Cabal know where he is. The Nod were a terrorist group who were trying to commit genocide as most of you know about Khan now. Well, Kane was the leader, and Khan was his second in command. He may have known where Kane was as well, but he did not get the chance to awaken his crew and awaken Kane. We don't know where Legion and Cabal have been hiding out but they're here to awaken Kane."

"And what's gonna happen when they awaken him?" Jim asked.

"If they succeed at awakening him…if he is somewhere out there, there will most likely be another war, but we have to stop him from using any tiberium he may have stored with him."

Jim rubbed his face as he sighed. "So, are you gonna tell us what tiberium does?"

"It turns people into his mindless warriors."

"Against their will?"

"Yes, and they become what is called brutes. The tiberium gives them incredible strength, plus, they are likely to awaken their augment army as well."

"You mean Khan's crew?"

"Exactly, and they will know where Kane is."

"And they're right there…" Jim did not even finish that sentence. Now that Legion and Cabal had taken control of headquarters, they had access to the area where those augments were kept.

"It's a bad situation, but we do have means to fight back," Winston declared.

Jim knew this was the war Admiral Marcus was referring to all the time. Our entire way of life will be decimated if I'm not in command. It was all making more sense now. A war of epic proportions that none of them knew was coming but Marcus knew all along.

Winston knew that Kirk most likely would put the whole thing together because he had been closer to the truth than anyone else. "One thing that is of utmost importance," Winston said. "That is stopping Kane from causing a tiberium explosion. It would attract the Scrin to Earth and there would be a war."

"Why would they be attracted to it? What do they have to do with this? And who are they?" Jim asked.

"The Scrin are weapons experts, they are ruthless in war, and if they come here, they will be virtually unstoppable."

"But they've been stopped before?"

"Yes. That's why we have to work fast. I'll take you all to the next chamber to see what we have to fight against this. If you'll join me…"

Admiral Winston left the meeting room, and the others followed him, along with Jim. As soon as Jim walked out of the room, his followers were around him. "Well?" Solan asked.

"We're in trouble," Jim replied.

"Explain, Admiral," Spock said.

"It's a lot to explain. I'll have to explain it to you later. Right now, we're about to see our arsenal. This all revolves around the situation with Khan who was part of some terrorist group called the Nod, and Starfleet sprang from what used to be the GDI, or global defense initiative. That Earth defense mechanism in space is housing some ion cannon. This is complicated, but those two who hijacked our ship are intending to wake up some Nod leader named Kane who intends to start a war here on this earth by setting off some tiberium explosion…" Jim explained as much as he could to them while they followed behind Admiral Winston.

As Jim and the crew entered the cavern, the lights came on. Jim stood there a moment with his mouth open as he looked around them. Admiral Winston just stood there a moment as he could see Jim's and the others' reactions of surprise. Doctor McCoy seemed to be in awe, and Spock was his usual self, although troubled. Solan looked rather angry as he observed the cavern.

"I can't believe this," Solan declared. "When are we gonna be told the entire truth?"

"You're about to be," Admiral Winston said. "And you're not gonna like it."

Jim shook his head. "Why all this secrecy? Don't you think it would be better for people to know the true history than to believe a lie and then it comes back to haunt you later, and you have a lot of people who have no idea what's going on?"

"I didn't make these rules."

"But you went along with them."

"We can't go back and change it now. All we can do is try and do something about this threat. Now, are you with me?"

Everyone looked at Jim to see what he would say. "Of course we're with you," he said.

Winston did not know whether it was good or disturbing that all the others seemed to soften with Jim's word. "Follow me then," he said. "We'll bring more people in on this later when we find them."

Jim looked at the enormous chamber where there was all sorts of war machines and weapons. "This is incredible," he said.

"I don't think I'd use that word," Bones grumbled. "How do we always get into these things?"

"Wrong place at the wrong time?"

"The story of our lives," Solan said.

"Yeah," Bones agreed. "We're definitely in the middle. Which way is out?"

"Will you guys just cool it?" Jim asked.

Helek snickered at that. "That's not easy to do," he said.

"Guys, we're not alone."

"Yes, he's afraid Admiral Winston will know we're a bunch of wise guys," Bones declared.

"He's embarrassed by his wise-cracking friends," Solan added.

Jim rolled his eyes at that. He could not believe there were actual tanks stored in this chamber, and some other odd-looking weapons that he had never seen. He could not believe what he was seeing. He had not wanted to believe that Cabal was telling the truth, but here they were…walking through what looked like a war museum. However, that was not the most fascinating part, because as they got past the war museum, they came to a cryotube.

"Oh brother," Bones said. "You remember what happened the last time we came upon a cryotube. We ended up almost crashing into the Earth."

"Will you relax?" Jim asked. He looked at Admiral Winston. "Who is this?"

"Michael McNeil. He was actually born in a Nod colony because his parents had been captured by them. They wanted to make him…well, what Khan became. Mac, as he was called, would have been in Khan's position but Mac and his brother were rescued and he was raised on GDI bases, and when he was old enough, he used his talents against the Nod. He was a very good soldier and was instrumental in defeating the Nod and the Scrin. His loyalty is without question, and he knows how to use all this equipment. That's why we have him here. He has innate knowledge of all this."

Jim looked at the frozen being inside the cryotube. "So, we're gonna wake up another being from the past having no idea what his reaction will be? Didn't we learn anything the last time?"

"Mac was nothing like Khan, and he had no love for the Nod and their twisted philosophies."

"But you only know this from hearsay."

Bones was studying the controls on the cryotube. "This is identical to the tubes that Khan and his bunch were in. Are you sure about this? He's another one of those super beings, isn't he?"

"I know what I'm talking about," Winston declared. "Doctor McCoy, if you'll thaw out our friend."

Bones looked at Jim for his approval, which Admiral Winston scowled at. Jim nodded. Bones began the awakening sequence. Spock stood beside Jim. "Jim, I believe I understand Doctor McCoy's concern," he said.

"Spock, we're being ordered by the head of Starfleet," Jim reminded him.

"I hope this does not land us in a worse situation. I am quite relieved that Uhura is on New Vulcan. I do believe she enjoys being there. She says it is peaceful."

"I wanted to get Carol and the kids on their way to Kronos, but I'm not sure that would work or be safe."

"You would be lucky if you could get them off the planet."

"We're gonna make these people pay, and we're gonna stop them no matter what."

"From what I read, that's not gonna be easy," Solan said.

Jim thought he could always expect Solan to study everything about a situation that he could find. He was quite an investigator. "I don't think they've ever met up with anyone like me," Helek said as his eyes were glowing and he had electricity jumping between his fingers.

"Probably not," Jim agreed. "But since Cabal has been in the system, he will most likely know your weaknesses."

Helek frowned. "He would know that about everyone."

Artie stepped closer then and cleared his throat. "I've been thinking about how we could get Cabal out of that system," he said.

"I'm listening," Jim replied.

"Well, how do you always get rid of a computer virus?"

Jim just stared at him a moment a little bewildered. Sure, he could do complicated math problems and make plans to defeat deranged villains but when it came to computer systems, he had to let someone else handle it. "I don't really know," he said.

"One of the easiest ways to do it is to quarantine the virus."

"Yeah…and how do you do that?"

"First you have to distinguish it and its location. Then you can trap it."

"But he's not really a virus."

"He's an alien computer program."

"How do you intend to stop him? I mean, he's intelligent and he's controlling the system."

"Yes, but he's not omniscient. We're gonna distract him. While you and others are working to defeat the visible enemy, I and my army will fight the invisible one. While one distracts him, the other will be the real threat."

"How do you intend to do that without communications?"

"My friend, there are other ways to communicate besides electronically."

Jim just stood there a moment. "That's good. I'm glad you can do that."

"When your battle begins, we'll begin ours when he's the most distracted."

"Right. You do that."

"So I have your permission?" Artie asked.

"Absolutely. I trust you."

"Thank you, Admiral."

Jim looked at Admiral Winston who had his arms folded. "You amaze me, Kirk," Winston said. "You manage to keep this crew loyal to you and you're not even their captain anymore."

"Admiral Kirk knows the strengths of the people who work for him," Spock said. "And he allows them to use those strengths."

"I see."

They heard a sound coming from the cryotube. "He should be thawed out in about thirty minutes," Bones said. "After being frozen this long, it has to be a slow process."

"I suppose I can show you around this place while we wait," Admiral Winston said.

"Why do I get the feeling you've been here before?" Jim asked.

"When I became head of Starfleet, I was shown everything, Admiral Kirk."

Jim frowned. "That means Admiral Marcus knew."

"Sure he knew. That's what he was always talking about…it wasn't with the Klingons. He thought he could force Khan to tell him where Kane was after he found the Botany Bay. You should have seen him. You would have thought he just found the key to peace in the galaxy."

"Instead, it was war."

"Exactly."

Jim remembered everything Admiral Marcus had done, and he could see how it was tied to all this now. He could remember him saying A war with the Klingons is inevitable. But Jim had a feeling that was not the one he was truly concerned about. He also knew why Marcus did not want Khan brought back to Earth for trial and why he intended to kill them. Khan would have told everything and might have even escaped.

Spock walked over to Jim. "May I know your thoughts on this matter, Jim?" he asked.

"Just remembering, Spock," Jim said. "You remember that you were even concerned about the fact that Khan wasn't getting a trial."

"I do. I believe we are seeing the reasons for that whole situation now."

"Yeah. It would have been nice to know then. I can't understand why Khan didn't tell me then. He told us about that ship."

"Yes, but he also knew you would be against the Nod. He would not have divulged that secret. He simply wanted to get back to Earth."

"But if he was loose on Earth before, why didn't he find Kane then?"

"I believe there was more motivation to his destroying that archive than was previously known." Spock looked at Admiral Winston. "Am I right, Sir?"

"I'm afraid so, Spock," Admiral Winston answered. "Like I shared with Admiral Kirk and the others, I never was for all the secrecy, but as you know, I was overruled." He began to walk, and Jim and the others followed him. "That so-called archive was actually a research center. Starfleet was researching Nod weapons, Scrin weapons and technology, even Tiberium. Thankfully, it wasn't liquid."

"Tiberium?" Spock asked.

"A very dangerous element, Mister Spock. It was Kane's main purpose to spread it."

"But why?"

"Tiberium is a crystal element that can grow roots and spread just like a plant."

"So it's alive?" Bones asked.

"Well, basically, yes. It spreads and can take over this planet."

"What does it do?"

"Anyone who comes in contact with it could become a mindless slave that they call a brute, or they can die. Otherwise…they can be like Khan or McNeil over there."

Jim looked at the cryotube and then back at Admiral Winston looking very confused. "Why are we waking up another guy like Khan?" he asked.

Bones and Spock both looked rather alarmed. "I assure you that he is nothing like Khan," Winston said. "His intelligence and…super abilities are equal, but he left the Nod and fought against them."

"And you're sure he won't betray us?" Jim asked.

"I'm positive. See, there was another reason Khan blew up that facility, and he most likely thought McNeil was in there. He also most likely thought there was liquid tiberium and he wanted to create a tiberium explosion that would have brought the Scrin to Earth."

"This gets worse all the time," Bones remarked.

"Who are the Scrin?" Solan asked.

"They're a warrior race from another galaxy," Winston said. "Whatever we do, we have to prevent them from getting to Earth."

"Or our entire way of life will be decimated," Jim added, remembering Marcus's words.

"And Khan did say that Marcus wanted to exploit his savagery," Spock reminded him.

Jim nodded. "He wanted to get that technology from Khan, and he had been getting it for three years. That's why Khan knew what was there, and he wanted to kill all those old admirals because they knew." Jim looked at Winston. "Am I right?"

"I'm only guessing like you are, Kirk," Winston replied.

Jim also remembered those chilling words: I was never gonna spare your crew. "He thought we knew the truth or would find it out," he said. "Starfleet used to be GDI, whatever that was then. Global Defense Initiative. But what did that entail?"

"It was in the days when Earth had a military. All I can tell you is what I've learned, but when McNeil is thawed out, he can tell you a lot more, but this computer system here contains the whole history, and it is on a completely different network."

Admiral Winston went over to the wall and flipped a large lever which activated a loud humming sound for a moment, and then more, brighter lights came on. He flipped another switch which brought the computer system to life. Artie walked over to it in front of the large screen. "This is incredible," he said. "It actually works." He watched the screen come to life and sat down in the seat in front of the keyboard.

"You know how to work this thing?" Jim asked.

Artie looked at Jim. "Oh, yes," he said with a smile and enthusiasm. "This system will help my plot against Cabal."

"Oh. How?"

Artie rubbed his hands together and cracked his knuckles. "You act like a kid with a new toy," Solan declared.

"I am. I am," Artie said.

Jim walked on with Admiral Winston. "I guess you have someone to run that computer for you," Jim said.

"If he can stop Cabal, it may make this a lot easier," Winston replied.

They sat down at a table which Jim thought looked like it was made from an old tank with part of the tank treads as the legs, and the top of it looked like it could have been made from some other part of the tank. "We all knew it could come to this one day," Winston said.

"But why?" Jim asked. "And where is this Kane? Do you think he's one of those frozen people who were with Khan?"

"No. He's not there. He's hidden somewhere untraceable. Starfleet had thought for years that Kane had escaped on the Botany Bay but when they were discovered, he wasn't there. So now we know he's somewhere else in a regeneration chamber. I'm sure Legion and Cabal know where. That's why we have to stop them. Their main goal will be to wake him up. And who knows how many he'll recruit? There are plenty of people who hate Starfleet, and most of them don't even know why."

"All this ties to Khan and why he wanted to destroy Starfleet. I can't understand why he didn't awaken Kane then."

"He didn't have the chance. If he had made it back to Earth and escaped, he would have done it while Starfleet was crippled. We're assuming he was aiming that ship at Starfleet headquarters. If he had succeeded, and if your crew had not been determined to stop him, who knows what would have happened? That's why I brought you here. You've been in more scraps than any other Admiral, even me."

"Thanks a lot."

"I think you're our ace in the hole."

Jim looked up at the ceiling of the chamber. "That is quite a description of it," he said.

"Kirk, this is probably the most important mission you've ever been on. The future of this planet and Starfleet depends on it."

"Yeah. I've been in this spot before. So, while we're on this mission, are we GDI or Starfleet?"

"Mr. Kirk, we will always be Starfleet, but we will fight when necessary. You should know that."

"Yes, Sir." Jim paused a moment. "Tell me something: was Admiral Marcus from that time? He had no qualms about sending us on that mission, and if I had not been really emotionally compromised, I would have listened to Mister Scott when he pointed out that it was a military operation. I think about all this now, and it makes a whole lot more sense. So, are we really explorers or are we a military? Right now, I'm having a hard time distinguishing that."

Admiral Winston was silent a moment. "I really don't know that much about Admiral Marcus and his past. But I do know that he had searched for the Botany Bay for years. He wanted to be the one who found Kane. It was why he always knew war was coming. He was really obsessed. He also knew with that Scrin technology, he could defeat the Klingons. Khan knew that too."

Jim could remember how Khan had beaten all those Klingons like a one-man army. "I knew that bombing at a library couldn't be all there was to it. And I asked about it during that meeting."

"He may have thought you would figure it out. He never had Starfleet approval for that mission."

"He intended to kill my whole crew."

"I remember hearing that recording. It was hard to believe. He did not intend for you to get back to Earth. It's still mind-boggling."

"I don't know how he disabled the warp drive, but it all makes sense now. It fits together like a puzzle."

"I must agree, Admiral," Spock said as he heard that. "I do believe that particular situation is becoming much clearer. I could not see the logic in Admiral Marcus's moves, nor Khan's moves, but now it makes more sense."

"What to do now is the question. How do we fight a computer program and an ancient being who can regenerate himself and who is going to do his best to draw some race of warrior bugs from another galaxy? And we don't even know where this guy is but some computer program with the help of a cyborg is going to bring him out of stasis."

"It is quite a complicated situation, but I believe we will do as we always have and will triumph."

"Let's hope."