I kind of massaged the age gap a bit here. Itachi is 12 and Sasuke is 6. Also, the entire story is outlined into three parts, in which the first and second will stand separate from the third. This story takes me a lot longer to write (as it's stressful for me to write scenes that are stressful to the characters), but I really like it.
Chapter 1: Fly-by-Night
"With all due respect, Danzou-sama, I cannot accept this mission."
There was silence for a moment. Thinking that this would not be the best time to look up from his kneeling position, Itachi focused on one of the cracks in the cold concrete floor. It meandered to the right until it intersected with another crack, making a shape like a shuriken where they met.
"Do you defy the council then, Uchiha?" Danzou said finally. Itachi pulled his attention away from the floor and looked up, but the Root leader's face was inscrutable, even for someone as good as reading people as the Uchiha prodigy.
"You know that I have the utmost loyalty to Konoha," Itachi replied calmly after collecting his thoughts for a moment. "I have done all that was asked of me and more. I would never refuse a mission if I felt it to be for the good of the village, but this...my own family...this is unthinkable."
Frowning, Danzou leaned back in his chair, toying with the scroll that held the mission details. Itachi watched him apprehensively. Those who defied Danzou often 'disappeared' discreetly—but he couldn't meekly obey this time. After a tense silence, Danzou was the first to speak. "Very well," he said, closing his eyes (the visible one, anyway) and waving Itachi away with one hand. "I understand. You may go."
A bit puzzled by his luck, but pleased that he had gotten away unscathed, Itachi stood and began to turn away. He caught a flash of movement in his peripheral vision just too late to dodge a blow that threw him to the floor as the other members of his ANBU team tackled him. Cursing himself for being stupid enough not to expect an attack, he turned on his sharingan and faced the first assailant, only to be pinned from behind and blindfolded by the other two.
"I sympathize with your attatchment to your family," he heard Danzou say as the Root leader's footsteps passed where Itachi was being restrained by his one-time comrades-in-arms. "You'll see them again soon...after your execution for their murder."
Itachi managed to snarl some very, very uncharitable things about Danzou's ancestry before he was knocked unconscious.
When he came to, he found himself chained to the wall of a high-security ANBU holding cell. All his weapons were gone, but his armor had not been stripped off, which was a relief. Unfortunately, all his attempts to reach his secret escape kit—a minute rice paper weapons-summoning scroll hidden in the flange of his breastplate—only got him bruised wrists and scraped fingers. At last, after several minutes of trying, he managed to catch the end between two fingers, but the fragile paper tore as he tugged on it. Mentally cursing the wretched object for wasting precious time (he had no idea how long he'd been out, he could already be to late) he forced himself to work more gently. Finally, after he had almost given up hope of ever getting the thing loose, it snapped out of the curve of metal that held it. Before Itachi could improve his grip on the scroll, however, it flew out of his grasp and landed in the far corner of the cell, where it burst open. Ducking away from the resultant shower of weapons, he hoped the noise would not attract the attention of a guard.
A senbon gleamed tantalizingly, just within reach of his foot. Just the ticket, Itachi thought, kicking it back to where he could reach it and start picking the lock on the shackles that held him. The senbon snapped off short, but not before a satisfying clink let him know that the catch had been released. With his now-free hand, Itachi grabbed another senbon and set to work on the other lock. As he could now turn to see what he was doing and had a much larger range of motion, it proved to be much less challenging than the first. Almost before it freed him, he was up and moving, gathering up as many kunai and shuriken as he could fit into his belt and pockets and flashing through the handseals required to blow the door out with a fireball.
Darting out of the cell and into the corridor, Itachi noted with surprise that there were no guards. Danzou must be very confident if he left someone as dangerous as the vaunted Uchiha prodigy unguarded—but then Danzou was nothing if not confident. The next thing Itachi noticed was rather more disturbing. Through the windows he could see dark sky and constellations, and it had only been mid-afternoon when he had been summoned to ANBU headquarters. When he first saw the orange glow against the night, he gave up on finding his way out through the winding corridors and leapt through one of the wide panes of glass, ignoring the sharp pang as one of the myriad slivers of glass cut his shoulder. Almost before he landed he was up again, vaulting across rooftops and perching atop a telephone pole from which he could see the Uchiha compound.
Danzou had not wasted his time.
All that Itachi could past the compound walls were flames, and he had a feeling it wouldn't be any better from a closer vantage point. Still, perhaps he could do something. ANBU couldn't have taken everyone by surprise—except that they could. Itachi was in ANBU, therefore the Uchiha had no reason to expect an attack from that quarter, not without some warning at least.
A shuriken whipped past Itachi's head, taking a few strands of hair with it. ANBU must still be around then; perhaps they had been expecting him to escape? Jumping down from the telephone pole to a nearby roof, he began to circle the compound, dodging the tagged kunai that his pursuer was throwing at him while trying to see if there was any building that hadn't gone up in flames yet.
The main house sat in the center of the compound. Before tonight, it had been nestled in a grove of Japanese maples and cherry trees, but the trees he had sparred under with Shisui were nothing but black, charred skeletons now. As far as he could see through the smoking trees, most of the main house had either collapsed or exploded, but a few rooms in the back still appeared to be standing. One of them was Sasuke's bedroom...praying that his little brother had stayed in his room instead of running outside and being cut down, Itachi vaulted into the compound.
It was horribly still inside the walls. The only sounds were Itachi's harsh breathing and the crackle of flames from the smoldering houses—Itachi knew what he would find if he searched and forced himself not to. Strangely, his ANBU pursuer had stopped attacking him, although Itachi could sense his chakra signature somewhere on the roofs behind him.
Ducking quickly through the charred trees surrounding what was left of his house, he shattered Sasuke's bedroom window and jumped inside, landing silently on the floor. The remnants of the house seemed to be holding together, but who knew how long that would last. The sudden collapse of the rest of the house must have smothered any flames, but the room was still filled with thick gray smoke.
Sasuke was nowhere to be seen. "Otouto!" Itachi called softly, coughing as he inhaled some of the smoke.
"Nii-san?" Sasuke's quiet answer and subsequent fit of coughs came from under the bed.
Itachi sighed in relief at the assurance his brother was still alive and promptly started choking on the smoke again. "It's safe, come on out," he said, kneeling down so he could reach under the bed to take Sasuke's hand and pull him out.
"Nii-san, what's going on?" Sasuke asked, looking around the smoke-filled room.
"I'll explain later, we have to get out of here." Itachi replied quickly. The ceiling had begun to creak ominously and he doubted it would hold much longer.
Sasuke was only wearing a thin nightshirt, but there was no time to get him dressed, so Itachi wrapped him in one of the quilts off the bed before picking him up. "Hold on to me," he ordered, beginning to form the first seal in the teleportation jutsu.
"Nii-san, wait!" Sasuke wailed, pounding on Itachi's armoured chest with soft fists and kicking hard enough that Itachi had to either set him down or risk dropping him.
"What is it?" Itachi snapped, losing his calm; the roof would go any moment and he was beginning to sense more chakra signatures outside.
"We have to save Risu-tan!" Sasuke announced determinedly before diving under the bed again.
Of course, save the poor innocent stuffed animal... Itachi thought, taking a family photograph from Sasuke's nightstand and tucking it behind his breastplate in the short time it took for Sasuke to retrieve his beloved toy.
Squirrel in hand now, Sasuke let Itachi drape the quilt around him and scoop him up again. "Ne, Nii-san, aren't Tou-san and Kaa-san coming with us?" he asked as Itachi again began the teleportation jutsu.
Itachi froze in mid-seal. "Sasuke, they...they can't..." frantically, he tried to think of a way to explain what had happened without breaking down himself. He had shut off the part of his brain that had realized the tragedy and he couldn't afford to release all the pent-up emotions now.
He had never expected to be relieved by an attack, but the tagged kunai suddenly flung through the window gave him the perfect excuse not to answer the question. Dropping to the floor, careful to shield Sasuke beneath him, he flashed through the rest of the seals in record time and felt the familiar tugging, rushing sensation as the jutsu activated a split second before the tags exploded, collapsing the rest of the house.
They fell to the grass somewhere which, as far as Itachi could tell, was outside Konoha proper and somewhat to the west. Sasuke was huddled into his chest, breathing raggedly; this was his first experience travelling this way, and Itachi knew how disorienting it could be until one got used to it. Still, there was no time to waste. They had to get moving, and that as quickly as possible.
Shifting his grip on Sasuke so that he had one hand free but was at no risk of dropping the child, Itachi bounded into the trees, picking up speed to the near-flying pace he was used to from ANBU missions. By the time he stopped, the moon had shifted position far enough that he felt sure no pursuers would be anywhere near them.
Carefully selecting a safe-looking but still easily defensible clearing, Itachi leapt down and gently nestled Sasuke in the roots of a massive oak tree before sitting protectively beside him. Twining his fingers absently into his sleeping brother's still baby-soft hair, he began to consider what options they had for the future.
Obviously, they would have to leave the Land of Fire entirely. With any luck, and if they kept moving, they would be believed dead and could remain in relative safety, but it would be difficult to have any kind of a livelihood.
Akatsuki was what worried him most. Until now, he had categorically refused their clandestine advances, but the clan could no longer shelter him. If it weren't for Sasuke, the logical choice would be to go to them (even if he hated what they stood for), but an international terrorist organization was no place for a child.
He was shocked out of his reverie when he realized that Sasuke's hair was no longer under his fingers. Instaneously alert, he whirled around only to see that Sasuke, now awake, had only moved over about a foot and was staring at him sulkily from behind his bangs. "Nii-san, stop petting me!"
Itachi, remembering how Sasuke had always hated his aunts (and various other female relatives) fussing over him at parties, did not press the issue. The thought of his relatives brought up a fresh pang of grief but he squelched it forcefully. "Sasuke, are you alright?"
Sasuke nodded. "I'm fine...only my eyes hurt."
Itachi was at his brother's side almost instantaneously. "Here, let me see," he said, brushing Sasuke's bangs out of his face and gently tilting his head back so the moonlight fell on his eyes—which were now blood red. "It's probably from the smoke," he lied, hoping Sasuke wouldn't see how worried he was. "Blink a few times and it should go away."
This was a new difficulty. The Sharingan had never been intended to be activated this early; while Itachi had attained his at a surprisingly young age, this was a bit of an anomaly. Sasuke was not a prodigy, and there was a very real risk of his going blind if he began to use the Sharingan, not to mention the added complication of the two of them remaining concealed.
Yawning, Sasuke put his arms around his brother's waist and promptly fell asleep again: Itachi decided that the worrying could wait—he had his brother and that was all that mattered.