Okay, there are two fics like this and one of them is only kinda like this but neither detail much about just how Jack got napped or, in the case of the other one, how he escaped, I'm hoping this will be different that either of those fics but they are the inspiration for this, so credit has to be given to the following pennames:

ToaXabineh and their fic: Long lost son

and

Inkcrafter and their fic: Not in blood, but in bond

Check those out too, they're good.

They hadn't seen them coming, not by a longshot. They were battling Decepticons, and winning, when it happened. No one was prepared. No one was in good enough shape to stay and fight. They were lucky so many of them got away. Though their loss was great. MECH had come with helicopters and tried capturing one of the 'bots or 'cons, but had failed. The ground bridges had been activated and Silas had seen the opportunity slipping away, fortunately humans were a lot slower than transformers. Or, unfortunately.

Jack had been right behind Miko and Raf, but the fact that he was behind them was his downfall, literally. A couple of MECH operatives tackled him to the ground and more were coming after the others. The two humans and Optimus, who hadn't yet entered the ground bridge, stopped and were about to come to his aid, but Jack wouldn't let them.

"Go!" he yelled, struggling against the two operatives trying to pin him down.

Optimus, being hardened by war, scooped up the two children and left, knowing all to well that they would have been taken captive had they stayed.

"Jack!" Miko and Raf yelled as Optimus ran into the portal, the scene disappearing from their sights.

Once the bridge closed Jack mentally relaxed, physically he still fought against the operatives holding him, until a familiar boot came down in front of him. The two MECH agents finally had him pinned to the ground, arms behind his back. Jack looked up to meet Silas' eyes and glared at the scarred man.

"Now, now Jack, no need to be so hostile." the man drawled, smirking.

That was the last Jack saw before he was hit in the head and the world faded into black.

That was three weeks and five place-switches later. Every time Silas got a hunch of the Autobots gettign closer he transported them somewhere else. Three weeks of nothing but pain. Jack had been subjected to torture by Silas personally, other times he was kept in a drugged state so that he wouldn't be able to escape. Unnkown to Silas, Jack was slowly but surely building up an immunity to the drug they were using. His moments of clarity got longer and longer and he used these moments to plan an escape. When he was dragged out of his cell to the room which Silas was using for his interrogation he memorised the way through the corridoors. When he was absolutely sure he knew the way there he risked looking around more every time. There were at least four places where he could escape from, he just had to wait until he had enough of an immunity to the drug before attempting anything.

The day he escaped he got lucky, only two MECH guards had come for him this time. As he pretended to be out of it as they dragged him along he stealthily withdrew a pocketknife from an inner pocket in his shirt, how it hadn't been detected was beyond him but he was not complaining. He silently flicked it open before stabbing the man to his left in the abdomen, as soon as the man let go he stabbed the other guard in the throat, almost vomiting when the blood made contact with his hand and face. Yanking the knife out he ran to the second escape point, since the first one was much too obvious. He picked up a chair and with all his might flung it against the small window he'd only just be able to crawl through, smashing the glass into hundreds of tiny shards. Without missing a beat Jack stepped onto the chair and crawled through the window, landing in a dirty alley. Looking around he could see it was night time where ever he was and he could hear someone enterign the code for the door right next to the window. He didn't have much time. He was weak from weeks of just enought food, if it could be called that, to survive and not being allowed or able to move made his escape all the more difficult. He couldn't run very fast and he'd used up most of his energy already. Seeing an uncovered manhole Jack made a split-second decision and jumped in, ignoring the cuts on his feet and hands from the shards of glass. The reason he had cuts on his feet too was because MECH had taken his shoes. As he climbed down the ladder he could hear yelling and footsteps drawing closer and was glad he'd been able to get the manhole cover back in it's place. Though with cuts on his feet they could probably follow the trail of blood. He was proven correct when just as he touched the bottom of the ladder the cover was being moved. Without looking back he darted away, his bare feet only barely making any sound. This was when the drugs completely wore off and all the damage done to his body made itself known. It became harder to move forward when it felt like every bruise, cut and welt was on fire, he knew it would only be a matter of time before they caught up to him. With this in mind Jack tried to make his communicator work, it was didguised as a digital watch on his wrist, Silas had seen no reason to deny him the knowledge of how long he'd been held and thus let him keep it, all the better for him. The watch actually held an emergency communication unit and sent a weak signal out at all times, this was how the Autobots had kept finding him, it also took his pulse, letting them know he was alive. The problem at the moment, however, was that it was using it's emergency battery, it was only sending out his pulse status, no weak tracker signal and no way to use the comm. With this revelation, Jack's pulse skyrocketed as he was about to round a corner. Before he could do that, however, he was tackled.

Leo, Don, Mikey and Raph had just been roaming around the sewers when they heard it. Faint footsteps followed by noisier footsteps. They'd went towards the sounds when they saw them, a young teen with no shoes and looking terrible and five black clad men, four of them wearing suits that covered all of their bodies, even their faces. The last one had nothing hiding his face and the four turtles could see his scarred face. They saw as the kid went down, face scraping against the concrete as he was pinned by one of the thugs.

"Now now, Jack. Why would you run? We were having so much fun together." the scarred man drawled, a smirk forming on his face.

"Your definition of fun differs from mine." the kid rasped as if he'd been using his voice too much for yelling.

"You know what I want Jack. Why won't you just give your friends' location and I'll let you go." the man said, rounding the teen and the man pinning him, looking Jack in the eyes.

The brothers could see the kid look at the man in defiance "You haven't gotten anything out of me after three weeks, why do you think that's gonna change any time soon?"

The four echanged a wide-eyed look, if what they thought the man meant by "fun" then this kid was really loyal to the guys this guy was trying to find. Leo nodded to his brothers, they were going to save this Jack from whoever these guys were. After a bunch of hand signals that would've looked completely irrelevant to anyone else, they striked.

Silas was smirking in that annoying way that made Jack want to spit on him. He wasn't able to due that, however, since his mouth and thoat were dry as a desert. Thus he settled on glaring at the evil man, not even bothering to fight against the painful hold the MECH agent had on him, he was too tired to move anymore. His breathing was becoming more and more laboured due to the pain and the weight of the man sitting on him. Jack could feel trickles of blood sliding from his cheek to his throat, thelling him that he had even more wounds now, joy. Just when he thought his escape was for nothing he heard the sound which accompanied a blade being unsheathed, a strange sound since: 1) they were in a sewer and 2) because MECH didn't use such primitive weapons. Before the black haired teen could reflect uopn that the weight on him suddenly disappeared accompanied by the sound of flesh hitting flesh, the grip on his wrists disappeared along with the man who'd tackled him. First his fingers twitched, then he slowly and painfully moved his arms under him and rolled to his side, not having any energy left. Glancing around himself the best he could revealed four MECH agents in a pile and Silas sporitn a slash accross his face which Jack hoped would scar too. The Silas was also downed and Jack felt himself being picked up. The last thing he saw before the exhaustion made him fall unconscious was a green shoulder, what looked like the edge of a turtle's shell and a strip of blue fabric.