Superboy was unconscious by the time they reached Batman's jet. His powerful body lay limp as Superman carried the smaller half-breed to the gurney in the back, laying him down gently to avoid spreading the toxic Kryptonite any further. Robin, Kid Flash, and Artemis filed in behind him, clearly shell-shocked by the encounter. While meeting Luthor and learning the truth about Superboy had completely blind-sided Kid Flash and Artemis, Robin was held captive by his own fear and guilt. It was his fault that Superboy had come here in the first place. He should have known this would happen…He didn't notice that he was trembling until he felt Wally's hand on his back comforting him. Wally was still clearly trying to process everything that had happened while he tried to smile soothingly to his friend. Robin's eyes were focused on his unconscious teammate before him. Superboy was pale and sweating profusely, his body doing everything it could to rid itself of the poison.
Superboy floated in and out of consciousness during their ride to Gotham. Voices and faces blurred in his mind… Everything seemed far away and distorted. Part of him could understand what was going on, but he couldn't process the information in the frontal lobe to give the situation rational thought. He could hear every voice from here to Star City along with countless noises he couldn't name; with his defenses lowered, he couldn't prevent his Kryptonian hearing taking over. He heard Robin's labored breathing leaning over him. He heard Superman's elevated heartbeat and the words he spoke to Batman in the cockpit.
"Batman…" Superman's voice was tinged with emotion… maybe, panic? "Batman, don't be like that. This isn't my fault. I didn't ask for a kid, or a clone, or whatever you call him in your head." Batman glanced back toward the cargo hold, ignoring the superhuman, before continuing to navigate the jet as though the other man hadn't spoken at all.
"Damnit, Bruce-"
"Shh," Batman silenced his friend, well-adjusted to the sensitivity of Kryptonian hearing. He nodded back toward the cargo hold where Superboy could hear every word, even if he couldn't process them. While it may have been obvious to Superman who Batman really was, Batman had since taken to lining his cowl to prevent another breach. Batman felt irritation rise in his throat. Emotions like this really have no place in crime fighting. Maybe Clark and Conner can get away with it, but it will get the rest of us killed, or worse.
When the heroes arrived back in Gotham they took a secret entrance into the Batcave. A normal looking building in a rougher part of the city retracted to reveal a narrow road leading into the dark. Batman flew over the road, quickly navigating a complicated series of turns before landing on the underground helipad. Superman carried Superboy out of the jet after everyone had exited. The cave was still further on, but there was no reason for Wally or Artemis to travel with them any further. For the sake of Batman's already damaged security, Kid Flash and Artemis were to head out the way they had come. Superboy's critical condition didn't allow much time for social niceties, but Superman agreed to transport Artemis home after he had transported the younger Kryptonian into the Batcave's medical wing.