Disclaimer: I don't own GI Joe.

*Note: This story follows the recently continued Larry Hama continuity. There is no Kamakura in this, as he appears in a different Joe canon universe and the story takes place time wise before he becomes Kamakura anyway. However, possible future fics in this AU verse may bring him in since the "Sean Collins" character was created by Hama and therefore technically exists in his universe, even if he isn't a ninja (yet). In the most recent issues of GI Joe: A Real American Hero, for those who haven't read the newest issues yet, Storm Shadow escaped from his brainwashing. Billy's mind was taken over by the digitally saved personality of Dr. Venom. Snake Eyes was brainwashed by the brainwave scanner, but was freed by Storm Shadow. Together, Snake Eyes and Storm Shadow freed Billy from his brainwashing and helped remove Dr. Venom from his mind. The Baroness also seems to have escaped from her brainwashing.

From here on out, this is obviously my own fan AU, which will pull primarily from the Hama verse and occasionally elements from the IDW and Devil's Due continuities. There also some slight changes that I have made. For instance, Doc is still alive in my continuity. I like the guy, so yeah, he's still here.

*Also, special thanks to willwrite4fics for both letting me bounce ideas off her and for her being my beta for this story.

Wearied of the war,
and by ill-fortune crushed, year after year,
the kings of Greece, by Pallas' skill divine,
build a huge horse, a thing of mountain size,
with timbered ribs of fir. They falsely say
it has been vowed to Heaven for safe return,
and spread this lie abroad. Then they conceal
choice bands of warriors in the deep, dark side,
and fill the caverns of that monstrous womb
with arms and soldiery.

Aeneid, by Vergil

Sleepers

Chapter 1: The Walls of Troy

The past.

He sat there. Minutes ticked by and still he sat, an immobile statue fixed in place as it waited for…something. A half empty cup of cold coffee, long forgotten, stood sentinel next to a slim folder, upon which a general's hat sat. There was an open file in front of the silent man.

"Sir?" A knock at the door drew his attention away from his musings. General Malthus, the leader of a secret cabal of generals known as "the Jugglers," looked up. Standing in the doorway was his faithful protégé, codenamed "Sinon" for the purposes of this particular project. Malthus was himself going by the codename "Odysseus."

Malthus eyed the folder in the other man's hands. He hoped that this was what he had been waiting for.

"Is that it?" the general asked. The other man nodded. Malthus took the folder and opened it up to find a detailed list of the incoming candidates for the GI Joe team. He studied each name intently and jotted down names to review further. As the general read through the roster, his eyes paused at a name. He looked at it for a while before a smile grew on his face.

"This one's perfect."

"I'll see to it, then," Sinon replied after he was shown the name. "I'll begin making the preparations."

General Malthus nodded. He leaned back in his chair and fought back a yawn. Project Odysseus was working out much better than he'd hoped. The program, of course, wasn't an "official" government program and would probably be considered "illegal." That didn't matter to the general, however. All records of the program would either be erased or deeply hidden. Everyone involved with it had been chosen specifically by him. Malthus trusted in their loyalty and commitment.

Less than two weeks later, the general stood quietly in the back of a large room and waited. He heard voices murmuring as three individuals made their way in his direction. The door opened to reveal Sinon and another agent, codenamed "Athena." Behind them was the GI Joe recruit, who had been summoned for a meeting by a superior officer. The soldier looked around with wary curiosity.

"Welcome," Malthus told the recruit. "You may refer to me as General Odysseus. I have a job for you."

The soldier gave him a questioning look.

Malthus smiled while he reassured the young soldier. They sat down at a small table. The general spoke with the soldier about the upcoming assignment with GI Joe. Athena served them all a cup of coffee, taking care to give the recruit one that had been spiked with a tasteless drug.

It took about two minutes for the drug to take effect. The GI Joe recruit's eyes opened wide when it became apparent that something wasn't right. However, by that point the soldier's body had become limp. Sinon easily carried the conscious, but immobile figure over to the station they had prepared. They had needed the soldier conscious, but unable to fight back. The soldier's eyes stared at a chair hidden in the back of the room. Arm and leg restraints very clearly stood out on it.

A pleased General Malthus watched as the conditioning began. Soon, this soldier would be one of many "recruits." Like the mythical Trojan horse, they would all bear a hidden soldier inside…though in this case, the soldier was a constructed personality that was hidden deep within a recruit's psyche. The sleepers of the Odysseus Project were completely loyal to Malthus and would occupy key positions that would give him access to information. If a situation developed that required direct action, the sleeper would fully activate and take matters into his or her hands.

Spies and assassins. They were the perfect tools, especially since the carriers were unaware of their passengers.

The initial programming took just over ten hours. Any longer than that and there would have been suspicions concerning the soldier's noticeable absence. Over the course of the next year, Malthus and his staff would coordinate their schedules for when recruit #31 had leave off base. "Refresher" implants further solidified and completed the programming.

For the next few years, Malthus's sleepers served him well. Recruit #31 had been accepted as a member of GI Joe. Once this had happened, the general allowed the sleeper to pick a codename, though its "carrier" remained unaware of the hidden passenger. Through his loyal soldier, the leader of the Jugglers was able to keep tabs on his associate, Clayton Abernathy. At least until…

A stunned Malthus looked down at the receipt in his hands. Destro bid him goodbye and left him to the media cameras, the angry Joes, and the United States government. All of his machinations to plant the blame for the Cobra Island fiasco onto Hawk and Hollingsworth had now failed. His own attempt to kill the two generals with a grenade and to discredit GI Joe had also failed. His unfortunate future was pretty much guaranteed.

He was condemned to several years in a Fort Leavenworth prison by a military court. When Malthus was led out of the courtroom, he briefly met the piercing eyes of the Joes' Tomahawk. They locked gazes for the longest of moments. A heavily armed MP forced him to keep moving. Hawk looked insufferably pleased as Malthus was led away.

The clank of the barred doors shut on him. Malthus sat. Like a lonely sentinel, the condemned military leader kept watch from his prison cell. Many of his secrets had been dragged out during his hearing. Hawk and Hollingsworth had managed to dig up quite a bit of dirt on Malthus. However, they hadn't found everything. There were many things that they were still unaware of.

A pair of dark eyes peered out of the prison cell bars. Malthus clasped both hands under his chin as he mused. There was nothing else for him to do in prison but think and plan.

His sleepers were still out there, his precious, loyal soldiers. General Malthus vowed to do whatever it took to regain control of his program and to prevent anyone else, particularly Hawk or even General Crowther, from getting their hands on it. When an opportunity eventually presented itself four years later, Malthus took it.

Now

"Oh, this is too rich."

Cobra Commander was in an excellent mood, all things considering. He'd unfortunately lost Storm Shadow and his son Billy. The Arashikage ninja had not only managed to escape, but with the help of the Joes, had freed a temporarily brainwashed Snake Eyes as well as Billy. The brainwave scanner's effect on the Baroness had also worn thin. If anything, Cobra Commander should still be in a raging fury.

Good news tended to change one's mood for the better and he had very good news. The terrorist leader smiled as he considered the newest piece of Intel, slipped to him by a former associate that was rotting in the Fort Leavenworth prison. Even now, Malthus was proving to be full of wonderful surprises.

"What have you found…"

"…that is so interesting…"

"…dear Cobra Commander?"

The arrival of the Crimson twins cemented his good mood. Tomax and Xamot were irritating to deal with at times, but they were loyal and trustworthy members of Cobra. Seeing as they were also the leaders of his Crimson Guard, Cobra Commander had good reason to confide in the two businessmen.

"Hawk's got a mole and he doesn't even know it," the Cobra leader explained cheerfully. He started laughing a moment later. This was too good. The Joes would never live this one down. Malthus was a genius.

The twins exchanged looks before giving him an identical raised eyebrow. Tomax sat down, followed shortly by Xamot. Cobra Commander waited impatiently for them to settle in before he began briefing them on his newest prize. Both men were all smiles once they realized the implication of what Cobra now had in its possession.

"Interesting," Tomax mused. "Very interesting indeed."

"I agree," Xamot added. "However, what do we do about Malthus? He's only given you a nugget. We've got the names of his sleepers, but we still don't know yet how to activate and use them."

"I know," Cobra Commander admitted. "Malthus is smart. He doesn't want his program to go to waste and he still wants to be in control of it. Our good general knows that we still need him."

"How did he even slip this out past the Leavenworth guards?" one of the twins asked. Cobra Commander tapped his finger on the table a moment before explaining. Malthus apparently still had many soldiers who were loyal to him. A high ranking military officer, who had only identified himself as "Sinon", had followed secret orders to deliver information to Cobra. Sinon had made it quite clear that Malthus expected Cobra's "assistance" in return for more information.

"I think we should arrange an escape for the dear general," Cobra Commander told his Crimson Guardsmen. "Get it done. Sinon won't cooperate further until we've gotten Malthus out."

"What do you plan to do once we've got Malthus out?" Xamot asked.

Cobra Commander debated on his answer. He'd been turning this over in his mind ever since Malthus's lapdog had given him information on Project Odysseus. The Joes' mole was very useful to him. He could keep the sleeper in place for now; however, this particular Joe was in a position to cause a lot of damage and chaos. Cobra Commander couldn't wait to see the look on Hawk's face when he found out what was underneath his nose. The terrorist leader cackled in glee at the thought.

"For now, we'll wait," Cobra Commander finally answered. "You can't rush a show as good as this. Malthus rolled a damned Trojan horse into the Pit and the horse doesn't even know it's got something hiding inside. It's a ticking time bomb waiting to go off and I didn't even put it there, but I'm sure as hell going to use it." That was the greatest irony of all. Cobra Commander hadn't planned for this particular weapon and had certainly not been expecting that something like it would fall into his lap. Now he had a good little soldier and spy to use as not only for physical work, but as a psychological weapon.

"Then?" Tomax ventured to ask. Cobra Commander smiled maliciously underneath his blue mask. Oh, but how he was going to savor the 'then' part. It was with great satisfaction that he answered the twins.

"We're going to burn down the walls of Troy and everyone inside. Or rather, we'll let our 'horse' do that."

Three weeks later.

"Well?"

General Hawk regarded the blonde psychiatrist standing next to him. For the moment, the two men were watching several ninja spar in the Pit dojo. As they looked on, Storm Shadow paused long enough to correct Billy's form. They resumed a few seconds later.

Psyche Out indicated his head towards the door and the general followed him out. As they had learned the hard way, Thomas Arashikage had very keen hearing. Lifeline and Doc were having a field day trying to figure out how the ninja had such above average hearing, which was nearly as sensitive as that of a dog. According to Snake Eyes, his sword brother had mastered an Arashikage technique known as the "Ear that Sees."

"They're all doing well, all things considering," the Joes' psychiatrist reported. "However, the mental and emotional wounds are deep. It will take time for all of them to recover, especially Billy and Storm Shadow." Those two in particular had been under Cobra mind control for years. Hawk nodded his head, having expected that those two would struggle more.

"Billy is having nightmares," Psyche Out continued. "And the occasional hallucination. I strongly suspect that Storm Shadow is as well, but so far he's not cooperating very well in our meetings. He refuses to admit to any of it."

"He'll cooperate if he wants to stay in GI Joe," Hawk replied. "I'll have another talk with him."

"If I may ask, what are you going to do about Billy?" Kenneth Rich asked. The Joe psychiatrist was very concerned about all of his patients, but he was particularly concerned about the youngest one.

"He'll stay for the moment," the general answered. They were still trying to determine what to do with Cobra Commander's son. The young man, nineteen years old now, was technically old enough to fight for his country if he wished. He'd had extensive training from Storm Shadow both during their brief interlude from Cobra, as well as during their brainwashing. Billy had already expressed interest in serving in GI Joe and both his mentor and Snake Eyes had supported the idea. Tommy was also adamant that he be able to continue his protégé's training.

There was also the issue that Billy was an automatic target. They could put him into protective custody, but Hawk strongly suspected that either Cobra would find him anyway, or the headstrong young man would try to find a way out of custody. Considering the extensive mental and emotional trauma that had been inflicted on him by the boy's so called father, it was far better to keep him at the Pit where Psyche Out could examine him. Hawk again doubted that Billy would willingly submit to the care of any other psychiatrist but a GI Joe one. There was too much of Thomas Arashikage in the young man, despite the fact that they shared no blood.

"Once you consider him fit for duty, I'll put him to work around the base," Hawk said. No doubt the boy would try to volunteer for missions, but for now, he was going to have to make do with things like guard duty. Besides, Beach Head had already made it quite clear that he thought Billy should train with the greenshirts since the young man hadn't had any military training. All of this of course meant that young William would be treated as the youngest soldier on base, even though he was a civilian and would also be treated as such. The kid couldn't exactly go through basic training without exposing himself to Cobra or making his unit a target.

Therefore, the short term solution was to keep Billy with the Joes and to occupy him with tasks that would keep him out of trouble for the time being. Hawk and his command staff weren't exactly happy with it, but it was what they had to do.

The two men separated after a few more minutes of discussion. General Hawk walked briskly through the halls of the underground GI Joe base. Men and women saluted him as he walked by. Clayton Abernathy gave them all respectful nod in return. The general felt his lips quirk up when he passed by a trio of Joes. Two of the three, Rock 'n Roll and Clutch, were supporting a limping Outback.

"Do I need to know what happened, gentlemen?" he asked dryly. He received three slightly alarmed looks and three negative shakes of the head. Hawk chuckled quietly as he walked by the three men. He commanded an elite group of men and women…all of whom had their own idiosyncrasies. Rock 'n Roll, Clutch, and Outback had no doubt been bored and had decided to do something "fun," resulting in unintended injuries. They were sure to get an earful from Doc and Lifeline.

Hawk chuckled again. He was certain that he commanded the strangest unit in the entire United States military, but he wouldn't trade any of them for the world. Clayton Abernathy felt that he was blessed that he could rightfully claim to be able to trust each and every soldier under his command with complete confidence. Even Storm Shadow, who had once been an enemy and was still struggling with the aftereffects of Cobra's brainwave scanner, had sworn an oath of loyalty to serve Hawk and the United States government.

The general trusted in the man's oath. As a ninja, Thomas Arashikage did not pledge his service to just anyone. This was especially true considering that the government had offered the ninja a deal that would wipe his criminal record clean in exchange for five years of military service.

A short beeping noise caught his attention. Hawk looked down at the small pager that had been tucked into a pocket. He pulled it out and saw a simple message. "Phone call."

Hawk walked into the Pit's communications center a few minutes later. Dial Tone was waiting patiently for him. The soldier handed him a phone. Clayton Abernathy was incredibly displeased to find General Crowther, the current leader of the Jugglers, on the other line.

"What do you want Crowther?" he asked with polite coldness. Hawk barely hid the snarl that threatened to burst out of his throat. Crowther was as corrupt as Malthus had been, only Crowther was doing a better job of being slightly more subtle about it. The man didn't actively try to raise Hawk's hackles, but he still went behind the back of the GI Joe general. The two men had butted heads more than once.

"We've got a problem," General Crowther told him. "We need to deal with it now." The man emphasized the word 'now.'

"I've got problems too. This had better be good," Hawk responded. The last thing he wanted was to get involved in some political infighting again, though he would do it if necessary. Hawk didn't want the pencil pushers at the Pentagon to suddenly decide to cut GI Joe's funding again.

"Not this big," the other man replied. "Malthus has escaped from Fort Leavenworth and it's entirely possible that Cobra helped him. However, we don't know what Cobra wants him for…if it WAS Cobra."

There was a long moment of silence as Hawk digested this newest information. He felt something nasty sink into the pit of his stomach. The last time he'd run into Malthus, the man had tried to blame him for something that had been out of his control, had managed to get him admitted to a psychiatric hospital on false pretenses, had then tried to discredit HIS Joes as out of control rogues, and then had tried to kill him. As if that wasn't enough, an appearance by Destro had confirmed that General Malthus had been dealing with Cobra behind all their backs.

"…Can you meet me tomorrow?" Hawk asked.

"I'm on the plane now. I'll be at the Pit in about three hours."

*Story note: The idea for Storm Shadow serving five years in the military in exchange for his records being wiped clean comes from Karama9's stories.