He's not the only one holding back, although Aqualad doesn't seem to feel the need to literally pull his punches to the same degree, trusting Superboy's Kryptonian heritage to let him take the hits. Instead, his restraint comes in the form of confining himself to fighting with his bare fists and feet, rather than using his sorcery. 

This handicaps him enough that, despite his greater experience, the fight is pretty obviously in Superboy's favor. It doesn't take long for an opening to come up that lets Superboy pin Aqualad to the wall. 

Hooray! And now that they are here he can communicate while Superboy seemingly pummels Aqualad!

"Everything born here is a slave, fight your way out and you'll be fighting the people you should be helping." Theatric slam, with a pulled punch. Hey, voice in his head, do they have a plan after the heroes appear defeated?

  Doctor Desmond won't kill them without say-so from his masters, and it will take time to speak with them. In that time you can help them escape.

Oh. Good. Good plan, voice in his head. "You're going to get captured-" punch that's set up to be the final one, "and then when no one's looking I come let you out."

Aqualad obligingly slumps against the wall. It's only half faked.

Internally, his mind reels. The Genomorphs are slaves to their creators, and Superboy wants to free all of them, not just himself. 

He was right. They are definitely in too deep. 

He's going to check on Kid Flash before he rips open the door. Not dead or critically injured, right?

(Though he's not sure that he'd know what to do with him if he were.)

Kid Flash was knocked unconscious when Superboy threw Robin into him. He doesn't seem to be too badly injured other than that. He's breathing, at least. 

Good!

This fact assured, he goes to open the door. He looks at the door panel, decides that approximately ten minutes of consciousness is not enough experience to figure out how to undo whatever arcane method the trio used to force it shut, and promptly rips through the door's lock with his hands like it's made out of jello instead of titanium alloy.

Dr Desmond, the G-Goblin Dubbilex, and the security officer, Guardian, are waiting beyond the door, along with another scientist who has been attempting to re-open it.

Desmond and Guardian each have a telepathic G-Gnome perched on one shoulder. 

Desmond, who is filed in Superboy's memory as a designated handler, steps up to the entrance and surveys the scene, taking in the crumpled and motionless bodies of the three young heroes. 

He smiles. "Atta boy." 

Designated handler, but definitely not the source of the voice that's been speaking to him this entire time. The voice felt close, though -

  I am here.

His eyes flick minutely to Dubbilex.

For a brief second, he locks eyes with a short, slim, horned creature. The Goblin-class Genomorph, created here to be an intelligent and loyal assistant for the real scientists. Capable of telekinesis and telepathy, able to coordinate with other Genomorphs in the base.

And, it seems, him. A sense of familiarity fills him.

And then his eyes flick away.

  Good. School your expression to blank neutrality. He must not know that you think.

He obeys, of course. Blank neutrality, a machine waiting for orders. That's him, yep. It's just as well, he needs to figure out what to do now, how best to handle the situation. This is more complicated than any of his simulations. He's used to receiving telepathic information, but maybe he should work on sending it. It's important that he learn as much of the situation as possible.

What will happen if he acts suspiciously?

  Our smaller G-Gnome brothers are not particularly smart, but they are engineered to be very telepathically powerful. With their help, he could simply walk you back to your pod and put you back to sleep.

... Ah.

  Quite. They will follow my commands as well as his, but his authority supersedes mine. For similar reasons, they cannot simply knock him out.

Anyone else they're keyed to obey?

  A few, but the others are away by this hour. It's why I drew the heroes here now - though perhaps I miscalculated, I thought they'd send people more... experienced.

This might be better. Has he called in backup?

  ... No. No he hasn't.

He resists the urge to smile. Good.

To all outward appearances, he stands like a good little clone, waiting for orders.

"Get them into containment pods," Desmond orders Guardian.

"I...need to make a call." 

Taking one last look around the room, he turns on his heel and strides away. 

Guardian nods crisply, and starts barking orders at G-Troll soldiers. 

"Hey, kid." He looks at Superboy. "Help me carry them to the lab." 

He can absolutely do that. Aqualad and Robin can both get picked up, one for each shoulder, so that no one else is close enough to spot any flaws in their acting.

Guardian picks up Kid Flash, who is legitimately unconscious, and leads the way. 

Each of the young superheroes is restrained and sealed in a pod similar to the one in which Superboy woke up, with the same transparent casing. Task completed, Guardian turns to leave, looking at Superboy to see if he will follow. 

"... My pod's broken," he says, in an affected small voice, thinking of his emotional state right after waking up for the first time. In a vaguely hopeful tone, like he's so glad to have a job: "I can stay here to guard them while it's being fixed?"

"Sure, kid," Guardian agrees, voice a little less harsh than before. 

"I'll get right on that."

He leaves, and Superboy is alone with his would-be rescuers, one of whom is still unconscious. 

He indulges in a small sigh of relief.

Okay, where are the cameras in this room?

Just one, near the door and pointing towards the three pods at the far end. 

"Ugh..." Robin, having noticed that they're alone, opens his eyes and does a decent impression of someone just waking up from unconsciousness. Sliding a miniature lockpick into one hand, he angles it around and starts working on the manacle clamped around his wrist. 

Heh. He thinks he likes Robin.

Hey, voice, are there microphones in this room?

  No. Their monitoring system is largely via G-Gnomes.

"Hey. Camera's behind me. No microphone present. I don't think anyone's paying attention, but there might be an alert somewhere if I just fry it."

"There will likewise be an alert if anyone notices our attempt to escape," Aqualad points out.

"We need to work quickly. Do you have a way of waking Kid Flash?" He looks to his right, where Kid Flash is hanging motionless in his restraints. 

"Uh, maybe. Let's see." Dubbilex?

In Kid Flash's mind, there is a voice:

WAKE UP.

Kid Flash snaps awake with a gasp, blinking and breathing hard. 

His eyes focus on Superboy, who is standing right in front of him. "What?" he demands. "What d'you want?"