Jon has black hair and blue eyes, so there is an 85% chance Bruce might adopt him by accident
Jon Kent sat on the edge of the bed in his new room. His elbows rested on his knees, head in his hands. He was staring off into space when Alfred knocked on the frame of the open door. “Master Jonathan” Alfred said tentatively “I brought you some lunch” He held out a tray with a sandwich and coke can. Jon gave a little start “Oh thanks Alfred” he said sheepishly “and I wish you’d stop calling me master” his nose crinkled up as he said that. Alfred smiled slightly “well young sir I am an old man with old habits, I’m afraid it’s something you’ll just have to get used to.” Alfred knew it was the wrong thing to say the moment it left his mouth.
Jon’s face fell, “They’re not coming back are they?” His voice was unbelievably sad and Alfred saw the shin in his eyes that meant a fresh round of tears. Alfred came into the room after carefully placing the sandwich tray onto the desk he sat on the bed next to Jon. “Now listen here young man. Your father is Superman and they’re nothing he can not do, and your mother is even more impressive. They will return you just have to have faith in them” It had been 4 weeks since the interdimensional attack and the last time anyone had seen Superman or Lois Lane. In his heart Alfred felt like he was lying. Jon nodded sadly but didn’t start to cry, which was a victory Alfred patted him on the shoulder and quietly left the boy to his thoughts.
He found found Bruce in the cave looking at the massive screen of the cat computer. “Anything Master Bruce?” He’d asked this question a thousand times and the answer was always. “Nothing yet Alfred” Bruce barely looked at him to say it. He leaned back in his seat and rubbed the bridge of his nose, He was bone tired, when Clark had first disappeared Bruce hadn’t slept for 4 days straight, looking looking. He still wasn’t sleeping much, but at least now Alfred reflected he was sleeping at least few hours every night and eating regular meals.
Bruce looked off into space for a moment before speaking. “Whenever I went missing in the past, Clark always said he wasn’t worried. That he knew I’d come back, that he’d know if I died. That Batman and Superman were so linked in the universe that he’d just know if there was ever a time where I wasn’t coming back” Bruce looked down at his hands studying them. “I always said that was ridicules. He was just projecting feelings backward.” Bruce took a deep shaky breath before going on. “This time though, it does feel different than all the other times he’s gone missing, Alfred I can’t shake the feeling I’m never going to see him again.”
He looked at Alfred and a whole wordless conversation passed between them. After a long moment Alfred nodded “I believe it would be beneficial to come up with a useful distract for young Master Johnathan” He said. He didn’t say ‘and for you as well’ but that hung unsaid between them. “Hm his father would kill me if I took him out as one of us, and god knows the kind of damage a barely trained meta human will do on the streets of Gotham” Only someone who knew him as well as Bruce did would have noticed the signs of annoyance coming from Alfred. “Sir, with all due respect, it’s been a month, you, Batman the greatest detective in the world, and all the other heroes haven’t found a single useful clue to where either of that boy’s parents are. It’s time we start facing the realities that they’re not coming back. If they’re not, then sir, we are that boy’s family, this family has a family business, a business that is in that boy’s blood as much as any of your sons” Bruce looked away but Alfred knew him well enough to know he’d made his point.
That night Jon trudged down the stars into the cave, he hadn’t set foot there since coming to live with Bruce a month ago. Batman stood in full uniform and Jon gulped. In a month he’d become much less intimidated why Bruce Wayne, but Batman still gave him chills. “Jon, I know your father would want your training to go on even while he’s away. I’ve been remiss in that area” Batman said emotionlessly. Jon stared at him stupidly “training?” he echoed. Batman fixed him with an icy look “this isn’t a vacation Jon” Jon nodded slowly. “You’re coming out with me” Jon’s eyes bugged out. “um okay, I’ll go get my costume” Jon said half turning toward the stairs.
“No” Bruce said firmly. Jon turned back confusion written on his face. “It would raise too many questions to have Superboy partnering with Batman.” Bruce said again with no emotion. “We’ll have to find something for you in the cave” He went on. Jon crossed his arms with the first flash of defiance, “I’m not wearing Damian’s hand-me-downs” he said sticking his chin out. A slight smile crossed Batman’s face, “no I was thinking Nightwing could find you something” Out of the shadows a figure in a black uniform with a blue symbol across his chest came into view. Damian’s older brother Dick, Damian talked about him a lot but Jon had never really met him. “Hi Jon” He said with a small wave. “Lets go over to my part of the cave see if we can’t fix you up with something.”
A few minutes later Jon was twisting back and forth in front of a mirror. He was wearing a mostly black costume, red stripes the mirror of the blue one’s on Nightwing’s costume, run down his arms and over his middle two fingers. The symbol on his chest was the same but repeated 3 times, the one in the middle linked with the stripes along his arms, a smaller one on top and a larger symbol on the bottom. It felt weird wearing a mask, it was red too, Dick had filled in the area around his eyes with eyeshadow the first time Jon wore any make up which was also strange. “So what am I gonna be Nightwing Jr if the bad guys ask?” Jon said looking at how skinny his arms looked in the skin tight suit.
Dick smiled at him in the mirror. “You know where the name Nightwing comes from?” he asked Jon shook his head, he’d just thought that it had come to Dick in the middle of a rainstorm at midnight or something. “Your dad, as it happens. I quit, well Bruce kinda fired me, from being Robin, long story. I was trying to figure things out, so I went to see your dad. He told me about these Kryptonian myths, about two heroes. Nightwing was one of them, he gave me my name.” Dick was standing right behind Jon now his hands on his shoulders Jon was blinking back tears at all this talk about his dad. “The other hero, his name was Flamebird, that’s you Jon” Jon nodded slowly “Flamebird” he said experimentally. “Nice to meet you Flamebird” Dick said with a smile holding out his hand “I’m Nightwing”